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Lancaster CL, Yalamanchili PS, Goldy JN, Leung SW, Corbett AH, Moberg KH. The RNA-binding protein Nab2 regulates levels of the RhoGEF Trio to govern axon and dendrite morphology. Mol Biol Cell 2024; 35:ar109. [PMID: 38985523 DOI: 10.1091/mbc.e24-04-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024] Open
Abstract
The Drosophila RNA-binding protein (RBP) Nab2 acts in neurons to regulate neurodevelopment and is orthologous to the human intellectual disability-linked RBP, ZC3H14. Nab2 governs axon projection in mushroom body neurons and limits dendritic arborization of class IV sensory neurons in part by regulating splicing events in ∼150 mRNAs. Analysis of the Sex-lethal (Sxl) mRNA revealed that Nab2 promotes an exon-skipping event and regulates m6A methylation on Sxl pre-mRNA by the Mettl3 methyltransferase. Mettl3 heterozygosity broadly rescues Nab2null phenotypes implying that Nab2 acts through similar mechanisms on other RNAs, including unidentified targets involved in neurodevelopment. Here, we show that Nab2 and Mettl3 regulate the removal of a 5'UTR (untranslated region) intron in the trio pre-mRNA. Trio utilizes two GEF domains to balance Rac and RhoGTPase activity. Intriguingly, an isoform of Trio containing only the RhoGEF domain, GEF2, is depleted in Nab2null nervous tissue. Expression of Trio-GEF2 rescues projection defects in Nab2null axons and dendrites, while the GEF1 Rac1-regulatory domain exacerbates these defects, suggesting Nab2-mediated regulation Trio-GEF activities. Collectively, these data indicate that Nab2-regulated processing of trio is critical for balancing Trio-GEF1 and -GEF2 activity and show that Nab2, Mettl3, and Trio function in a common pathway that shapes axon and dendrite morphology.
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Affiliation(s)
- Carly L Lancaster
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322
| | - Pranav S Yalamanchili
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
| | - Jordan N Goldy
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322
| | - Sara W Leung
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
| | - Anita H Corbett
- Department of Biology, Emory College of Arts and Sciences, Atlanta, GA 30322
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
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2
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Li D, Huang Y. Regulated circRNA nuclear export in neuronal differentiation. Trends Cell Biol 2024:S0962-8924(24)00119-3. [PMID: 38964955 DOI: 10.1016/j.tcb.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024]
Abstract
Multiple mechanisms have been reported for how circular RNAs (circRNAs) are exported to the cytoplasm. A recent paper by Cao et al. shows that export of a subset of circRNAs with (A)-rich motifs, including one with a clear function, is regulated during neuronal development via a novel mechanism.
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Affiliation(s)
- Da Li
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06520, USA; Center of Reproductive Medicine, National Health Commission Key Laboratory of Advanced Reproductive Medicine and Fertility, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yingqun Huang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06520, USA.
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3
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Luo J, Yang Y, Zhang G, Fang D, Liu K, Mei Y, Wang F. Energy stress-induced circDDX21 promotes glycolysis and facilitates hepatocellular carcinogenesis. Cell Death Dis 2024; 15:354. [PMID: 38773094 PMCID: PMC11109331 DOI: 10.1038/s41419-024-06743-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/23/2024]
Abstract
Cancer cells undergo metabolic reprogramming in response to hostile microenvironments, such as energy stress; however, the underlying mechanisms remain largely unclear. It is also unknown whether energy stress-responsive circular RNA (circRNA) is involved in the regulation of glucose metabolism. Here we report that circDDX21 is upregulated in response to glucose deprivation by the transcription factor c-Myc. Functionally, circDDX21 is shown to promote glycolysis by increasing PGAM1 expression. Mechanistically, circDDX21 interacts with the RNA binding protein PABPC1, disrupting its association with the ubiquitin E3 ligase MKRN3. This disassociation attenuates MKRN3-mediated PABPC1 ubiquitination and enhances the binding of PABPC1 to PGAM1 mRNA, thereby leading to PGAM1 mRNA stabilization. The ability of the circDDX21-PGAM1 axis to promote hepatocellular carcinogenesis is validated in a xenograft mouse model. Additionally, in clinical hepatocellular carcinoma tissues, there is a positive correlation between circDDX21 and PGAM1 expression. These findings establish circDDX21 as an important regulator of glycolysis and suggest circDDX21 as a potential therapeutic target for hepatocellular carcinoma.
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Affiliation(s)
- Jingjing Luo
- The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yang Yang
- The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Guang Zhang
- The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Debao Fang
- The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Kaiyue Liu
- The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yide Mei
- The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Fang Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China.
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4
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Wang J, Zhu H, Gan J, Liang G, Li L, Zhao Y. Engineered mRNA Delivery Systems for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308029. [PMID: 37805865 DOI: 10.1002/adma.202308029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/05/2023] [Indexed: 10/09/2023]
Abstract
Messenger RNA (mRNA)-based therapeutic strategies have shown remarkable promise in preventing and treating a staggering range of diseases. Optimizing the structure and delivery system of engineered mRNA has greatly improved its stability, immunogenicity, and protein expression levels, which has led to a wider range of uses for mRNA therapeutics. Herein, a thorough analysis of the optimization strategies used in the structure of mRNA is first provided and delivery systems are described in great detail. Furthermore, the latest advancements in biomedical engineering for mRNA technology, including its applications in combatting infectious diseases, treating cancer, providing protein replacement therapy, conducting gene editing, and more, are summarized. Lastly, a perspective on forthcoming challenges and prospects concerning the advancement of mRNA therapeutics is offered. Despite these challenges, mRNA-based therapeutics remain promising, with the potential to revolutionize disease treatment and contribute to significant advancements in the biomedical field.
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Affiliation(s)
- Ji Wang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Haofang Zhu
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jingjing Gan
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Gaofeng Liang
- Institute of Organoids on Chips Translational Research, Henan Academy of Sciences, Zhengzhou, 450009, China
| | - Ling Li
- Department of Endocrinology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Yuanjin Zhao
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Institute of Organoids on Chips Translational Research, Henan Academy of Sciences, Zhengzhou, 450009, China
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5
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Mofayezi A, Jadaliha M, Zangeneh FZ, Khoddami V. Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1837. [PMID: 38485452 DOI: 10.1002/wrna.1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Ahmadreza Mofayezi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- ReNAP Therapeutics, Tehran, Iran
| | - Mahdieh Jadaliha
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Vahid Khoddami
- ReNAP Therapeutics, Tehran, Iran
- Pediatric Cell and Gene Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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6
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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.
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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.
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7
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Wang QH, Yan PC, Shi LZ, Teng YJ, Gao XJ, Yao LQ, Liang ZW, Zhou MH, Han W, Li R. PABPN1 functions as a predictive biomarker in colorectal carcinoma. Mol Biol Rep 2023; 51:40. [PMID: 38158471 DOI: 10.1007/s11033-023-08936-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE PABPN1 acts as a modulator of poly(A) tail length and alternative polyadenylation. This research was aimed to explore the role of PABPN1 in colorectal cancer (CRC). METHODS Public databases were performed to analyze expression, location, roles of prognosis and tumor immunity and interaction with RNAs and proteins of PABPN1. To investigate PABPN1 expression in tissues, 78 CRC specimens were collected to conduct IHC, and 30 pairs of frozen CRC and corresponding adjacent normal tissues were used to conduct qRT-PCR and WB. In addition, in vitro experiments were then carried out to identify the role of PABPN1 in CRC. RESULTS Compared with normal tissues, PABPN1 expression was significant higher in CRC. Its high level predicted poor outcome of CRC. Th1 and Treg had significant negative relationships not only with PABPN1 expression, but also with six molecules interacting with PABPN1, including IFT172, KIAA0895L, RECQL4, WDR6, PABPC1 and NCBP1. In addition, PABPN1 had negative relationships with quite a few immune markers, such as CSF1R, IL-10, CCL2 and so on. In cellular experiments, silencing PABPN1 inhibited proliferation and promoted apoptosis in HCT-116 CRC cells. CONCLUSION In summary, PABPN1 might become a novel biomarker and correlate with tumor immunity in CRC.
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Affiliation(s)
- Qing-Hua Wang
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Pei-Ci Yan
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Li-Zhou Shi
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Ya-Jie Teng
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Xiao-Jiao Gao
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Li-Qian Yao
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Zhi-Wei Liang
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Ming-Hui Zhou
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Wei Han
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China.
| | - Rui Li
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China.
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8
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Wang X, Zhou R, Lu X, Dai S, Liu M, Jiang C, Yang Y, Shen Y, Wang Y, Liu H. Identification of nonfunctional PABPC1L causing oocyte maturation abnormalities and early embryonic arrest in female primary infertility. Clin Genet 2023; 104:648-658. [PMID: 37723834 DOI: 10.1111/cge.14425] [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: 06/07/2023] [Revised: 08/10/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023]
Abstract
Oocyte maturation arrest, fertilization failure, and early embryonic arrest are important causes of female infertility, whereas the genetic events that contribute to these processes are largely unknown. Loss-of-function of PABPC1L in mice has been suggested to cause female infertility involved in the absence of mature oocytes or embryos in vivo or in vitro. However, the role of PABPC1L in human female reproduction remains largely elusive. In this study, we identified a homozygous missense mutation (c.536G>A, p.R179Q) and a compound heterozygous mutation (c.793C>T, p.R265W; c.1201C>T, p.Q401*) in PABPC1L in two unrelated infertile females characterized by recurrent oocyte maturation abnormalities and early embryonic arrest. These variants resulted in nonfunctional PABPC1L protein and were associated with impaired chromatin configuration and transcriptional silencing in GV oocytes. Moreover, the binding capacity of mutant PABPC1L to mRNAs related to oocyte maturation and early embryonic development was decreased significantly. Our findings revealed novel PABPC1L mutations causing oocyte maturation abnormalities and early embryonic arrest, confirming the essential role of PABPC1L in human female fertility.
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Affiliation(s)
- Xiang Wang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ruixi Zhou
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiaowei Lu
- Reproductive Medicine Centre, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Siyu Dai
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Mohan Liu
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Chuan Jiang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yanting Yang
- Medical Genetics Department/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ying Shen
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, China
| | - Yan Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Hanmin Liu
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, China
- Department of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, China
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9
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Subedi S, Nag N, Shukla H, Padhi AK, Tripathi T. Comprehensive analysis of liquid-liquid phase separation propensities of HSV-1 proteins and their interaction with host factors. J Cell Biochem 2023. [PMID: 37796176 DOI: 10.1002/jcb.30480] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/08/2023] [Accepted: 09/17/2023] [Indexed: 10/06/2023]
Abstract
In recent years, it has been shown that the liquid-liquid phase separation (LLPS) of virus proteins plays a crucial role in their life cycle. It promotes the formation of viral replication organelles, concentrating viral components for efficient replication and facilitates the assembly of viral particles. LLPS has emerged as a crucial process in the replication and assembly of herpes simplex virus-1 (HSV-1). Recent studies have identified several HSV-1 proteins involved in LLPS, including the myristylated tegument protein UL11 and infected cell protein 4; however, a complete proteome-level understanding of the LLPS-prone HSV-1 proteins is not available. We provide a comprehensive analysis of the HSV-1 proteome and explore the potential of its proteins to undergo LLPS. By integrating sequence analysis, prediction algorithms and an array of tools and servers, we identified 10 HSV-1 proteins that exhibit high LLPS potential. By analysing the amino acid sequences of the LLPS-prone proteins, we identified specific sequence motifs and enriched amino acid residues commonly found in LLPS-prone regions. Our findings reveal a diverse range of LLPS-prone proteins within the HSV-1, which are involved in critical viral processes such as replication, transcriptional regulation and assembly of viral particles. This suggests that LLPS might play a crucial role in facilitating the formation of specialized viral replication compartments and the assembly of HSV-1 virion. The identification of LLPS-prone proteins in HSV-1 opens up new avenues for understanding the molecular mechanisms underlying viral pathogenesis. Our work provides valuable insights into the LLPS landscape of HSV-1, highlighting potential targets for further experimental validation and enhancing our understanding of viral replication and pathogenesis.
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Affiliation(s)
- Sushma Subedi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
- Department of Zoology, North-Eastern Hill University, Shillong, India
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10
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Zhai H, Qin W, Dong S, Yang X, Zhai X, Tong W, Liu C, Zheng H, Yu H, Kong N, Tong G, Shan T. PEDV N protein capture protein translation element PABPC1 and eIF4F to promote viral replication. Vet Microbiol 2023; 284:109844. [PMID: 37572396 DOI: 10.1016/j.vetmic.2023.109844] [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: 06/20/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Porcine epidemic diarrhea (PED) is an acute, highly infectious intestinal disease caused by the porcine epidemic diarrhea virus (PEDV), which seriously endangers the healthy development of the pig industry. PEDV N protein is the most abundant viral structural protein, which can be combined with viral genomic RNA to form ribonucleoprotein complexes, thereby participating in the transcription and replication of the virus. However, how PEDV hijacks the host transcription translation system to promote viral proliferation remains unclear. In this study, we found that there is an interaction between PEDV N, polyadenylate-binding protein cytoplasmic 1 (PABPC1) and eukaryotic initiation factor 4F (eIF4F) proteins through coimmunoprecipitation, GST pulldown and fluorescence microscopy experiments. PABPC1 could bind to the poly(A) tail of the mRNA, and eIF4F could bind to the 5' end cap structure of the mRNA, so the interaction of PABPC1 and eIF4F could facilitate mRNA forming a circular shape to promote translation to the proteins. To further explore the effect of N protein capture protein translation element PABPC1 and eIF4F on PEDV replication, we overexpressed PABPC1, eIF4F (containing eIF4A, eIF4E and eIF4G) separately on Vero cells and LLC-PK1 cells, and we found that the PABPC1 and eIF4F protein could promote PEDV replication. Taken together, our data suggested that PEDV N protein promoted cyclization of viral mRNA carried by N protein through binding with PABPC1 and eIF4F proteins, thus promoting viral transcription and facilitating viral replication.
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Affiliation(s)
- Huanjie Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wenzhen Qin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Sujie Dong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xinyu Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xueying Zhai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
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11
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Han W, Shi CT, Chen H, Zhou Q, Ding W, Chen F, Liang ZW, Teng YJ, Shao QX, Dong XQ. Role of LncRNA MIR99AHG in breast cancer: Bioinformatic analysis and preliminary verification. Heliyon 2023; 9:e19805. [PMID: 37809464 PMCID: PMC10559167 DOI: 10.1016/j.heliyon.2023.e19805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/27/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Objective This research was aimed to preliminarily explore the clinical roles and potential molecular mechanisms of MIR99AHG and its significant transcripts in breast cancer (BRCA). Methods Public databases were utilized to analyze the expression and prognostic roles of MIR99AHG and its transcripts. Relationships between MIR99AHG expression and immune cells infiltration were analyzed in Xiantao platform. In addition, co-expressed genes and interacting proteins of MIR99AHG were predicted. CancerSEA analyzed its relationship with functional states. Next, CNV status, DNA methylation, interacting transcription factors (TFs) and ceRNA network were analyzed to explore its possible mechanisms. Then, RNA ISH and FISH assays were used to detect its expression and location in BRCA tissues and cell lines, respectively. Finally, qRT-PCR was utilized to investigate MIR99AHG expression in cell lines. Results Compared with the corresponding normal tissues, MIR99AHG expression levels were lower in all BRCA subtypes, and luminal B's was the lowest one. And MIR99AHG expression was negatively related to the tumor stage. In addition, 4 transcripts (ENST00000619222.4, ENST00000418813.6, ENST00000602901.5 and ENST00000453910.5) of MIR99AHG showed significant differences in the expression. Databases also suggested that the high MIR99AHG expression levels indicated good prognosis, especially in patients without lymph node metastasis. Xiantao found that MIR99AHG was positively related to 17 immune cells and negatively linked with 2 immune cells. CancerSEA analysis showed no relationships between MIR99AHG and functional states. From GEPIA and BCIP databases, 19 co-expressed genes were highly related to these four significant transcripts of MIR99AHG. StarBase, RNAct and HDOCK showed that several tumor-associated proteins, including U2AF65, hnRNPC, AEBP2, CHIC1 and so on, might interact with MIR99AHG. Genetically, BRCA had a higher proportion of MIR99AHG CNV loss than CNV gain, and the high level of DNA methylation indicated a good prognosis. Furthermore, 19 TFs were predicted to combine with the promoter of MIR99AHG. Then, we screened out 10 miRNAs potentially interacting with the significant transcripts of MIR99AHG, and five were significantly increased in breast tumors compared to normal tissues, including miR-194-5p, miR-320 b and so on, which could combine 14 mRNAs. Through ISH and FISH assays, we verified that MIR99AHG was down-regulated in BRCA samples and cell lines in comparison to non-tumor tissues and mammary epithelial cell line (MCF10A), and MIR99AHG was located both in cytoplasm and nucleus. qRT-PCR assay also showed the lower expression of MIR99AHG in breast cancer cells than that in MCF10A. Conclusion These results indicate that MIR99AHG can be a favorable prognostic indicator for BRCA. ENST00000619222.4, ENST00000418813.6, ENST00000602901.5 and ENST00000453910.5 are significant transcripts and their down-regulation may play crucial roles in the progression of BRCA.
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Affiliation(s)
- Wei Han
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, PR China
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Chun-tao Shi
- Department of General Surgery, Wuxi Xishan People's Hospital, Wuxi, Jiangsu, 214000, PR China
| | - Hua Chen
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Qin Zhou
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Wei Ding
- Ultrasonic Department, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Fang Chen
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Zhi-wei Liang
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Ya-jie Teng
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, 215300, PR China
| | - Qi-xiang Shao
- Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China
| | - Xiao-qiang Dong
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, PR China
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12
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Guan WL, Jiang LL, Yin XF, Hu HY. PABPN1 aggregation is driven by Ala expansion and poly(A)-RNA binding, leading to CFIm25 sequestration that impairs alternative polyadenylation. J Biol Chem 2023; 299:105019. [PMID: 37422193 PMCID: PMC10403730 DOI: 10.1016/j.jbc.2023.105019] [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: 03/08/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/10/2023] Open
Abstract
Poly(A)-binding protein nuclear 1 (PABPN1) is an RNA-binding protein localized in nuclear speckles, while its alanine (Ala)-expanded variants accumulate as intranuclear aggregates in oculopharyngeal muscular dystrophy. The factors that drive PABPN1 aggregation and its cellular consequences remain largely unknown. Here, we investigated the roles of Ala stretch and poly(A) RNA in the phase transition of PABPN1 using biochemical and molecular cell biology methods. We have revealed that the Ala stretch controls its mobility in nuclear speckles, and Ala expansion leads to aggregation from the dynamic speckles. Poly(A) nucleotide is essential to the early-stage condensation that thereby facilitates speckle formation and transition to solid-like aggregates. Moreover, the PABPN1 aggregates can sequester CFIm25, a component of the pre-mRNA 3'-UTR processing complex, in an mRNA-dependent manner and consequently impair the function of CFIm25 in alternative polyadenylation. In conclusion, our study elucidates a molecular mechanism underlying PABPN1 aggregation and sequestration, which will be beneficial for understanding PABPN1 proteinopathy.
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Affiliation(s)
- Wen-Liang Guan
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Fang Yin
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
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13
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Solodushko V, Fouty B. Terminal hairpins improve protein expression in IRES-initiated mRNA in the absence of a cap and polyadenylated tail. Gene Ther 2023; 30:620-627. [PMID: 36828937 PMCID: PMC9951143 DOI: 10.1038/s41434-023-00391-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/26/2023]
Abstract
Synthesizing mRNA in vitro is a standard and simple procedure. Adding the 5' cap and 3' polyadenylated (poly(A)) tail to make this mRNA functional for use as a vaccine or therapy increases the time and cost of production and usually decreases the yield, however. We designed mRNA that lacked a cap and poly(A) tail but included an internal ribosomal entry site (IRES) to initiate protein translation. To protect the 5' and 3' ends of mRNA from exonucleases, we added stable terminal hairpins. When compared against typical mRNA (i.e., mRNA that contained a cap and poly(A) tail but lacked hairpins), expression of the delivered reporter protein in HEK293 cells was similar. Using a triple instead of a single hairpin at each end increased protein expression even more. This method has the potential to simplify the production and reduce the cost of synthesizing exogenous mRNA for use as biologics or vaccines.
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Affiliation(s)
- Victor Solodushko
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
| | - Brian Fouty
- Department of Pharmacology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Center for Lung Biology, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- Department of Internal Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
- The Division of Pulmonary and Critical Care Medicine, University of South Alabama School of Medicine, Mobile, AL, 36688, USA.
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14
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Rouhana L, Edgar A, Hugosson F, Dountcheva V, Martindale MQ, Ryan JF. Cytoplasmic Polyadenylation Is an Ancestral Hallmark of Early Development in Animals. Mol Biol Evol 2023; 40:msad137. [PMID: 37288606 PMCID: PMC10284499 DOI: 10.1093/molbev/msad137] [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: 12/02/2022] [Revised: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3'-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in nonanimal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, and cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs, and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.
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Affiliation(s)
- Labib Rouhana
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Fredrik Hugosson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Valeria Dountcheva
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
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15
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Navickas A, Asgharian H, Winkler J, Fish L, Garcia K, Markett D, Dodel M, Culbertson B, Miglani S, Joshi T, Yin K, Nguyen P, Zhang S, Stevers N, Hwang HW, Mardakheh F, Goga A, Goodarzi H. An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus. Nat Cell Biol 2023; 25:892-903. [PMID: 37156909 PMCID: PMC10264242 DOI: 10.1038/s41556-023-01141-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/27/2023] [Indexed: 05/10/2023]
Abstract
Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis; however, its effects on cancer progression remain poorly understood. Here, to address this, we used ribosome profiling to compare genome-wide translation efficiencies of poorly and highly metastatic breast cancer cells and patient-derived xenografts. We developed dedicated regression-based methods to analyse ribosome profiling and alternative polyadenylation data, and identified heterogeneous nuclear ribonucleoprotein C (HNRNPC) as a translational controller of a specific mRNA regulon. We found that HNRNPC is downregulated in highly metastatic cells, which causes HNRNPC-bound mRNAs to undergo 3' untranslated region lengthening and, subsequently, translational repression. We showed that modulating HNRNPC expression impacts the metastatic capacity of breast cancer cells in xenograft mouse models. In addition, the reduced expression of HNRNPC and its regulon is associated with the worse prognosis in breast cancer patient cohorts.
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Affiliation(s)
- Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Institut Curie, CNRS UMR3348, INSERM U1278, Orsay, France
| | - Hosseinali Asgharian
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Lisa Fish
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Daniel Markett
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Bruce Culbertson
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Sohit Miglani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Tanvi Joshi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Keyi Yin
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Phi Nguyen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Steven Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Nicholas Stevers
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Hun-Way Hwang
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Faraz Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Andrei Goga
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
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16
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Kwiatek L, Landry-Voyer AM, Latour M, Yague-Sanz C, Bachand F. PABPN1 prevents the nuclear export of an unspliced RNA with a constitutive transport element and controls human gene expression via intron retention. RNA (NEW YORK, N.Y.) 2023; 29:644-662. [PMID: 36754576 PMCID: PMC10158996 DOI: 10.1261/rna.079294.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/12/2023] [Indexed: 05/06/2023]
Abstract
Intron retention is a type of alternative splicing where one or more introns remain unspliced in a polyadenylated transcript. Although many viral systems are known to translate proteins from mRNAs with retained introns, restriction mechanisms generally prevent export and translation of incompletely spliced mRNAs. Here, we provide evidence that the human nuclear poly(A)-binding protein, PABPN1, functions in such restrictions. Using a reporter construct in which nuclear export of an incompletely spliced mRNA is enhanced by a viral constitutive transport element (CTE), we show that PABPN1 depletion results in a significant increase in export and translation from the unspliced CTE-containing transcript. Unexpectedly, we find that inactivation of poly(A)-tail exosome targeting by depletion of PAXT components had no effect on export and translation of the unspliced reporter mRNA, suggesting a mechanism largely independent of nuclear RNA decay. Interestingly, a PABPN1 mutant selectively defective in stimulating poly(A) polymerase elongation strongly enhanced the expression of the unspliced, but not of intronless, reporter transcripts. Analysis of RNA-seq data also revealed that PABPN1 controls the expression of many human genes via intron retention. Notably, PABPN1-dependent intron retention events mostly affected 3'-terminal introns and were insensitive to PAXT and NEXT deficiencies. Our findings thus disclose a role for PABPN1 in restricting nuclear export of intron-retained transcripts and reinforce the interdependence between terminal intron splicing, 3' end processing, and polyadenylation.
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Affiliation(s)
- Lauren Kwiatek
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Anne-Marie Landry-Voyer
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Mélodie Latour
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Carlo Yague-Sanz
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
| | - Francois Bachand
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada J1E 4K8
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17
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Peerapen P, Chanthick C, Thongboonkerd V. Quantitative proteomics reveals common and unique molecular mechanisms underlying beneficial effects of caffeine and trigonelline on human hepatocytes. Biomed Pharmacother 2023; 158:114124. [PMID: 36521247 DOI: 10.1016/j.biopha.2022.114124] [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: 07/24/2022] [Revised: 11/26/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Caffeine and trigonelline are the major bioactive compounds in coffee. Caffeine alone or combined with other coffee compounds shows hepatoprotective effects. However, molecular mechanisms underlying such hepatoprotective effects remain unclear. We therefore addressed molecular effects of caffeine and trigonelline on human hepatocytes using quantitative proteomics followed by bioinformatic analyses to obtain topological and functional significance. HepG2 cells were treated with 100 μM caffeine or trigonelline for 24-h and evaluated by quantitative proteomics using nanoLC-ESI-LTQ-Orbitrap MS/MS. A total of 26 and 25 significantly altered proteins were identified in caffeine-treated and trigonelline-treated cells, respectively, compared with control cells. Topological analyses revealed that ribosomal and translation regulatory proteins predominantly served as the hub proteins associated with protein clusters. Functional analyses also revealed that these two bioactive compounds shared some molecular mechanisms via induction of translational processes. There were also other unique molecular functions and biological processes triggered or suppressed by either caffeine or trigonelline. These data highlight common and unique molecular mechanisms underlying the hepatoprotective effects of caffeine and trigonelline that may be useful for future clinical applications.
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Affiliation(s)
- Paleerath Peerapen
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanettee Chanthick
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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18
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Sidorova TV, Kutyrev IA, Khabudaev KV, Sukhanova LV, Zheng Y, Dugarov ZN, Mazur OE. Comparative transcriptomic analysis of the larval and adult stages of Dibothriocephalus dendriticus (Cestoda: Diphyllobothriidea). Parasitol Res 2023; 122:145-156. [PMID: 36370234 DOI: 10.1007/s00436-022-07708-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
Abstract
Tapeworms of the genus Dibothriocephalus are widely distributed throughout the world, some of which are agents of human diphyllobothriasis, one of the most important fish-borne zoonoses caused by a cestode parasite. Genomic and transcriptomic data can be used to develop future diagnostic tools and epidemiological studies. The present work focuses on a comparative analysis of the transcriptomes of adult and plerocercoid D. dendriticus and the identification of their differentially expressed genes (DEGs). Transcriptome assembly and analysis yielded and annotated 35,129 unigenes, noting that 16,568 (47%) unigenes were not annotated in known databases, which may indicate a unique set of expressed transcripts for D. dendriticus. A total of 8022 differentially expressed transcripts were identified, including 3225 upregulated and 4797 downregulated differentially expressed transcripts from the plerocercoid and adult animals. The analysis of DEGs has shown that among the most differentially expressed genes, there are important genes characteristic of each stage. Thus, several genes are characteristic of D. dendriticus plerocercoids, including fatty acid-binding protein and ferritin. Among the most highly expressed DEGs of the adult stage of D. dendriticus is the Kunitz-type serine protease inhibitor, in two putative isoforms. The analyses of GO and KEGG metabolic pathways revealed that a large number of the DEGs of D. dendriticus are associated with the biosynthesis of various substances such as arginine and folate, as well as with various metabolic pathways such as galactose metabolism, selenocompound metabolism, and phosphonate and phosphinate metabolism. This will contribute to further research aimed at identifying targets for new generation drugs and the development of specific vaccines.
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Affiliation(s)
- Tuyana Valeryevna Sidorova
- Institute of General and Experimental Biology, Siberian Branch of Russian Academy of Sciences, 670047, Ulan-Ude, Russia.,Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, 664033, Russia
| | - Ivan Alexandrovich Kutyrev
- Institute of General and Experimental Biology, Siberian Branch of Russian Academy of Sciences, 670047, Ulan-Ude, Russia.
| | | | | | - Yadong Zheng
- Zhejiang A&F University, Zhejiang Province, Hangzhou, China
| | - Zhargal Nimaevich Dugarov
- Institute of General and Experimental Biology, Siberian Branch of Russian Academy of Sciences, 670047, Ulan-Ude, Russia
| | - Olga Evgenievna Mazur
- Institute of General and Experimental Biology, Siberian Branch of Russian Academy of Sciences, 670047, Ulan-Ude, Russia
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19
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Qi Y, Wang M, Jiang Q. PABPC1--mRNA stability, protein translation and tumorigenesis. Front Oncol 2022; 12:1025291. [PMID: 36531055 PMCID: PMC9753129 DOI: 10.3389/fonc.2022.1025291] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
Mammalian poly A-binding proteins (PABPs) are highly conserved multifunctional RNA-binding proteins primarily involved in the regulation of mRNA translation and stability, of which PABPC1 is considered a central regulator of cytoplasmic mRNA homing and is involved in a wide range of physiological and pathological processes by regulating almost every aspect of RNA metabolism. Alterations in its expression and function disrupt intra-tissue homeostasis and contribute to the development of various tumors. There is increasing evidence that PABPC1 is aberrantly expressed in a variety of tumor tissues and cancers such as lung, gastric, breast, liver, and esophageal cancers, and PABPC1 might be used as a potential biomarker for tumor diagnosis, treatment, and clinical application in the future. In this paper, we review the abnormal expression, functional role, and molecular mechanism of PABPC1 in tumorigenesis and provide directions for further understanding the regulatory role of PABPC1 in tumor cells.
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Affiliation(s)
- Ya Qi
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University, Shenyang, Liaoning, China
| | - Min Wang
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University, Shenyang, Liaoning, China
| | - Qi Jiang
- Second Department of Clinical Medicine, China Medical University, Shenyang, Liaoning, China
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20
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Dai XX, Pi SB, Zhao LW, Wu YW, Shen JL, Zhang SY, Sha QQ, Fan HY. PABPN1 functions as a hub in the assembly of nuclear poly(A) domains that are essential for mouse oocyte development. SCIENCE ADVANCES 2022; 8:eabn9016. [PMID: 36306357 PMCID: PMC9616507 DOI: 10.1126/sciadv.abn9016] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Growing oocytes store a large amount of maternal mRNA to support the subsequent "maternal-zygotic transition" process. At present, it is not clear how the growing oocytes store and process the newly transcribed mRNA under physiological conditions. In this study, we report non-membrane-bound compartments, nuclear poly(A) domains (NPADs), as the hub for newly transcribed mRNA, in developing mouse oocytes. The RNA binding protein PABPN1 promotes the formation of NPAD through its N-terminal disordered domain and RNA-recognized motif by means of liquid phase separation. Pabpn1-null growing oocytes cannot form NPAD normally in vivo and have defects in stability of oocyte growing-related transcripts and formation of long 3' untranslated region isoform transcripts. Ultimately, Pabpn1fl/fl;Gdf9-Cre mice are completely sterile with primary ovarian insufficiency. These results demonstrate that NPAD formed by the phase separation properties of PABPN1-mRNA are the hub of the newly transcribed mRNA and essential for the development of oocytes and female reproduction.
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Affiliation(s)
- Xing-Xing Dai
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuai-Bo Pi
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jing-Ling Shen
- Institute of Life Sciences, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Song-Ying Zhang
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qian-Qian Sha
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317 Guangzhou, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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21
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Yang E, Huang S, Jami-Alahmadi Y, McInerney GM, Wohlschlegel JA, Li MMH. Elucidation of TRIM25 ubiquitination targets involved in diverse cellular and antiviral processes. PLoS Pathog 2022; 18:e1010743. [PMID: 36067236 PMCID: PMC9481182 DOI: 10.1371/journal.ppat.1010743] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/16/2022] [Accepted: 07/15/2022] [Indexed: 11/19/2022] Open
Abstract
The tripartite motif (TRIM) family of E3 ubiquitin ligases is well known for its roles in antiviral restriction and innate immunity regulation, in addition to many other cellular pathways. In particular, TRIM25-mediated ubiquitination affects both carcinogenesis and antiviral response. While individual substrates have been identified for TRIM25, it remains unclear how it regulates diverse processes. Here we characterized a mutation, R54P, critical for TRIM25 catalytic activity, which we successfully utilized to "trap" substrates. We demonstrated that TRIM25 targets proteins implicated in stress granule formation (G3BP1/2), nonsense-mediated mRNA decay (UPF1), nucleoside synthesis (NME1), and mRNA translation and stability (PABPC4). The R54P mutation abolishes TRIM25 inhibition of alphaviruses independently of the host interferon response, suggesting that this antiviral effect is a direct consequence of ubiquitination. Consistent with that, we observed diminished antiviral activity upon knockdown of several TRIM25-R54P specific interactors including NME1 and PABPC4. Our findings highlight that multiple substrates mediate the cellular and antiviral activities of TRIM25, illustrating the multi-faceted role of this ubiquitination network in modulating diverse biological processes.
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Affiliation(s)
- Emily Yang
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Serina Huang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Gerald M. McInerney
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Melody M. H. Li
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California, United States of America
- AIDS Institute, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail:
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22
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Fan X, Yang Y, Chen C, Wang Z. Pervasive translation of circular RNAs driven by short IRES-like elements. Nat Commun 2022; 13:3751. [PMID: 35768398 PMCID: PMC9242994 DOI: 10.1038/s41467-022-31327-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/09/2022] [Indexed: 12/30/2022] Open
Abstract
Some circular RNAs (circRNAs) were found to be translated through IRES-driven mechanism, however the scope and functions of circRNA translation are unclear because endogenous IRESs are rare. To determine the prevalence and mechanism of circRNA translation, we develop a cell-based system to screen random sequences and identify 97 overrepresented hexamers that drive cap-independent circRNA translation. These IRES-like short elements are significantly enriched in endogenous circRNAs and sufficient to drive circRNA translation. We further identify multiple trans-acting factors that bind these IRES-like elements to initiate translation. Using mass-spectrometry data, hundreds of circRNA-coded peptides are identified, most of which have low abundance due to rapid degradation. As judged by mass-spectrometry, 50% of translatable endogenous circRNAs undergo rolling circle translation, several of which are experimentally validated. Consistently, mutations of the IRES-like element in one circRNA reduce its translation. Collectively, our findings suggest a pervasive translation of circRNAs, providing profound implications in translation control. Unbiased screen of random sequences identified many short IRES-like elements to drive circular RNA translation and hundreds of rolling circle translation events, suggesting a pervasive cap-independent translation in human transcriptome.
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Affiliation(s)
- Xiaojuan Fan
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yun Yang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China.,CirCode BioMedicine, Pudong, Shanghai, China
| | - Chuyun Chen
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China
| | - Zefeng Wang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai, China. .,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
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23
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Nicholson-Shaw AL, Kofman ER, Yeo GW, Pasquinelli A. Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms. Nucleic Acids Res 2022; 50:4685-4702. [PMID: 35438785 PMCID: PMC9071453 DOI: 10.1093/nar/gkac263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/14/2022] Open
Abstract
The poly(A)-tail appended to the 3'-end of most eukaryotic transcripts plays a key role in their stability, nuclear transport, and translation. These roles are largely mediated by Poly(A) Binding Proteins (PABPs) that coat poly(A)-tails and interact with various proteins involved in the biogenesis and function of RNA. While it is well-established that the nuclear PABP (PABPN) binds newly synthesized poly(A)-tails and is replaced by the cytoplasmic PABP (PABPC) on transcripts exported to the cytoplasm, the distribution of transcripts for different genes or isoforms of the same gene on these PABPs has not been investigated on a genome-wide scale. Here, we analyzed the identity, splicing status, poly(A)-tail size, and translation status of RNAs co-immunoprecipitated with endogenous PABPN or PABPC in human cells. At steady state, many protein-coding and non-coding RNAs exhibit strong bias for association with PABPN or PABPC. While PABPN-enriched transcripts more often were incompletely spliced and harbored longer poly(A)-tails and PABPC-enriched RNAs had longer half-lives and higher translation efficiency, there are curious outliers. Overall, our study reveals the landscape of RNAs bound by PABPN and PABPC, providing new details that support and advance the current understanding of the roles these proteins play in poly(A)-tail synthesis, maintenance, and function.
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Affiliation(s)
| | - Eric R Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- UCSD Stem Cell Program, Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- UCSD Stem Cell Program, Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
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24
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Jungers CF, Djuranovic S. Modulation of miRISC-Mediated Gene Silencing in Eukaryotes. Front Mol Biosci 2022; 9:832916. [PMID: 35237661 PMCID: PMC8882679 DOI: 10.3389/fmolb.2022.832916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression is regulated at multiple levels in eukaryotic cells. Regulation at the post-transcriptional level is modulated by various trans-acting factors that bind to specific sequences in the messenger RNA (mRNA). The binding of different trans factors influences various aspects of the mRNA such as degradation rate, translation efficiency, splicing, localization, etc. MicroRNAs (miRNAs) are short endogenous ncRNAs that combine with the Argonaute to form the microRNA-induced silencing complex (miRISC), which uses base-pair complementation to silence the target transcript. RNA-binding proteins (RBPs) contribute to post-transcriptional control by influencing the mRNA stability and translation upon binding to cis-elements within the mRNA transcript. RBPs have been shown to impact gene expression through influencing the miRISC biogenesis, composition, or miRISC-mRNA target interaction. While there is clear evidence that those interactions between RBPs, miRNAs, miRISC and target mRNAs influence the efficiency of miRISC-mediated gene silencing, the exact mechanism for most of them remains unclear. This review summarizes our current knowledge on gene expression regulation through interactions of miRNAs and RBPs.
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25
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Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol 2022; 23:93-106. [PMID: 34594027 PMCID: PMC7614307 DOI: 10.1038/s41580-021-00417-y] [Citation(s) in RCA: 173] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
In eukaryotes, poly(A) tails are present on almost every mRNA. Early experiments led to the hypothesis that poly(A) tails and the cytoplasmic polyadenylate-binding protein (PABPC) promote translation and prevent mRNA degradation, but the details remained unclear. More recent data suggest that the role of poly(A) tails is much more complex: poly(A)-binding protein can stimulate poly(A) tail removal (deadenylation) and the poly(A) tails of stable, highly translated mRNAs at steady state are much shorter than expected. Furthermore, the rate of translation elongation affects deadenylation. Consequently, the interplay between poly(A) tails, PABPC, translation and mRNA decay has a major role in gene regulation. In this Review, we discuss recent work that is revolutionizing our understanding of the roles of poly(A) tails in the cytoplasm. Specifically, we discuss the roles of poly(A) tails in translation and control of mRNA stability and how poly(A) tails are removed by exonucleases (deadenylases), including CCR4-NOT and PAN2-PAN3. We also discuss how deadenylation rate is determined, the integration of deadenylation with other cellular processes and the function of PABPC. We conclude with an outlook for the future of research in this field.
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26
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Lisy S, Rothamel K, Ascano M. RNA Binding Proteins as Pioneer Determinants of Infection: Protective, Proviral, or Both? Viruses 2021; 13:v13112172. [PMID: 34834978 PMCID: PMC8625426 DOI: 10.3390/v13112172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 12/18/2022] Open
Abstract
As the first intracellular host factors that directly interact with the genomes of RNA viruses, RNA binding proteins (RBPs) have a profound impact on the outcome of an infection. Recent discoveries brought about by new methodologies have led to an unprecedented ability to peer into the earliest events between viral RNA and the RBPs that act upon them. These discoveries have sparked a re-evaluation of current paradigms surrounding RBPs and post-transcriptional gene regulation. Here, we highlight questions that have bloomed from the implementation of these novel approaches. Canonical RBPs can impact the fates of both cellular and viral RNA during infection, sometimes in conflicting ways. Noncanonical RBPs, some of which were first characterized via interactions with viral RNA, may encompass physiological roles beyond viral pathogenesis. We discuss how these RBPs might discriminate between an RNA of either cellular or viral origin and thus exert either pro- or antiviral effects—which is a particular challenge as viruses contain mechanisms to mimic molecular features of cellular RNA.
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Affiliation(s)
- Samantha Lisy
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.L.); (K.R.)
| | - Katherine Rothamel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.L.); (K.R.)
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Manuel Ascano
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.L.); (K.R.)
- Correspondence: ; Tel.: +1-615-875-8714
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27
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Assis LA, Santos Filho MVC, da Cruz Silva JR, Bezerra MJR, de Aquino IRPUC, Merlo KC, Holetz FB, Probst CM, Rezende AM, Papadopoulou B, da Costa Lima TDC, de Melo Neto OP. Identification of novel proteins and mRNAs differentially bound to the Leishmania Poly(A) Binding Proteins reveals a direct association between PABP1, the RNA-binding protein RBP23 and mRNAs encoding ribosomal proteins. PLoS Negl Trop Dis 2021; 15:e0009899. [PMID: 34705820 PMCID: PMC8575317 DOI: 10.1371/journal.pntd.0009899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/08/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022] Open
Abstract
Poly(A) Binding Proteins (PABPs) are major eukaryotic RNA-binding proteins (RBPs) with multiple roles associated with mRNA stability and translation and characterized mainly from multicellular organisms and yeasts. A variable number of PABP homologues are seen in different organisms however the biological reasons for multiple PABPs are generally not well understood. In the unicellular Leishmania, dependent on post-transcriptional mechanisms for the control of its gene expression, three distinct PABPs are found, with yet undefined functional distinctions. Here, using RNA-immunoprecipitation sequencing analysis we show that the Leishmania PABP1 preferentially associates with mRNAs encoding ribosomal proteins, while PABP2 and PABP3 bind to an overlapping set of mRNAs distinct to those enriched in PABP1. Immunoprecipitation studies combined to mass-spectrometry analysis identified RBPs differentially associated with PABP1 or PABP2, including RBP23 and DRBD2, respectively, that were investigated further. Both RBP23 and DRBD2 bind directly to the three PABPs in vitro, but reciprocal experiments confirmed preferential co-immunoprecipitation of PABP1, as well as the EIF4E4/EIF4G3 based translation initiation complex, with RBP23. Other RBP23 binding partners also imply a direct role in translation. DRBD2, in contrast, co-immunoprecipitated with PABP2, PABP3 and with RBPs unrelated to translation. Over 90% of the RBP23-bound mRNAs code for ribosomal proteins, mainly absent from the transcripts co-precipitated with DRBD2. These experiments suggest a novel and specific route for translation of the ribosomal protein mRNAs, mediated by RBP23, PABP1 and the associated EIF4E4/EIF4G3 complex. They also highlight the unique roles that different PABP homologues may have in eukaryotic cells associated with mRNA translation.
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Affiliation(s)
- Ludmila A. Assis
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
- Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Moezio V. C. Santos Filho
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
- Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Joao R. da Cruz Silva
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Maria J. R. Bezerra
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | - Kleison C. Merlo
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Fabiola B. Holetz
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Paraná, Brazil
| | - Christian M. Probst
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Paraná, Brazil
| | - Antonio M. Rezende
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Barbara Papadopoulou
- CHU de Quebec Research Center and Department of Microbiology-Infectious Disease and Immunology, Laval University, Quebec, Quebec, Canada
| | | | - Osvaldo P. de Melo Neto
- Department of Microbiology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
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28
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An T, Deng L, Wang Y, Yang Z, Chai C, Ouyang J, Lu X, Zhang C. The prognostic impacts of PABPC1 expression on gastric cancer patients. Future Oncol 2021; 17:4471-4479. [PMID: 34420428 DOI: 10.2217/fon-2021-0101] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To assess the prognostic impacts of PABPC1 on gastric cancer (GC) patients. Methods: The expression levels of PABPC1 in GC tissues and normal gastric tissues were initially compared via bioinformatics analysis. Immunohistochemical staining was accomplished to assess the expression of PABPC1 in the included GC patients. Then the impacts of PABPC1 expression on survival of GC patients were evaluated by Cox regression and Kaplan-Meier analyses. Results: The expression levels of PABPC1 in gastric tissues were significantly higher than those in normal gastric tissues (paired, p = 0.002; unpaired, p = 3.60e-9). By Kaplan-Meier, it was demonstrated that high expression of PABPC1 was significantly associated with worse overall and disease-free survival. Furthermore, high PABPC1 expression was demonstrated to be an independent predictive factor for both overall (p = 0.013; hazard ratio = 2.058; 95% CI: 1.162-3.644) and disease-free (p = 0.018; hazard ratio = 2.284; 95% CI: 1.153-4.524) survival. Conclusion: PABPC1 is a potential prognostic biomarker for GC patients.
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Affiliation(s)
- Tailai An
- Center of Digestive Diseases, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080,China
| | - Lingna Deng
- Department of Pathology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong518107, China
| | - Yan Wang
- Department of Radiology, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Zheng Yang
- Department of Hepatobiliary Surgery, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Cuicui Chai
- Department of Hepatobiliary Surgery, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Jun Ouyang
- Center of Digestive Diseases, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China.,Department of Pathology, Qingyuan People's Hospital, Qingyuan, Guangdong, 511518, China; Center of Scientific Research, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xiaofang Lu
- Department of Hepatobiliary Surgery, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, China
| | - Changhua Zhang
- Center of Digestive Diseases, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
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29
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Xiang K, Bartel DP. The molecular basis of coupling between poly(A)-tail length and translational efficiency. eLife 2021; 10:66493. [PMID: 34213414 PMCID: PMC8253595 DOI: 10.7554/elife.66493] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/21/2021] [Indexed: 01/10/2023] Open
Abstract
In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in Xenopus oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. Thus, strong coupling requires limiting PABPC, implying that in coupled systems longer-tail mRNAs better compete for limiting PABPC. In addition to expressing excess PABPC, post-embryonic mammalian cell lines had two other properties that prevented strong coupling: terminal-uridylation-dependent destabilization of mRNAs lacking bound PABPC, and a regulatory regime wherein PABPC contributes minimally to TE. Thus, these results revealed three fundamental mechanistic requirements for coupling and defined the context-dependent functions for PABPC, which promotes TE but not mRNA stability in coupled systems and mRNA stability but not TE in uncoupled systems. Cells are microscopic biological factories that are constantly creating new proteins. To do so, a cell must first convert its master genetic blueprint, the DNA, into strands of messenger RNA or mRNA. These strands are subsequently translated to make proteins. Cells have two ways to adjust the number of proteins they generate so they do not produce too many or too few: by changing how many mRNA molecules are available for translation, and by regulating how efficiently they translate these mRNA molecules into proteins. In animals, both unfertilized eggs and early-stage embryos lack the ability to create or destroy mRNAs, and consequently cannot adjust the number of mRNA molecules available for translation. These cells can therefore only regulate how efficiently each mRNA is translated. They do this by changing the length of the so-called poly(A) tail at the end of each mRNA molecule, which is made up of a long stretch of repeating adenosine nucleotides. The mRNAs with longer poly(A) tails are translated more efficiently than those with shorter poly(A) tails. However, this difference disappears in older embryos, when both long and short poly(A) tails are translated with equal efficiency, and it is largely unknown why. To find out more, Xiang and Bartel studied frog eggs, and discovered that artificially raising levels of a protein that binds poly(A) tails, also known as PABPC, improved the translation of short-tailed mRNAs to create a situation in which both short- and long-tailed mRNAs were translated with near-equal efficiency. This suggested that short- and long-tailed mRNAs compete for limited amounts of the translation-enhancing PABPC, and that long-tailed mRNAs are better at it than short-tailed mRNAs. Further investigation revealed that eggs also had to establish the right conditions for PABPC to enhance translation and had to protect mRNAs not associated with PABPC from being destroyed before they could be translated. Overall, Xiang and Bartel found that in eggs and early embryos, PABPC and poly(A) tails enhanced the translation of mRNAs but did not influence their stability, whereas later in development, they enhanced mRNA stability but not translation. This research provides new insights into how protein production is controlled at different stages of animal development, from unfertilized eggs to older embryos. Understanding how this process is regulated during normal development is crucial for gaining insights into how it can become dysfunctional and cause disease. These findings may therefore have important implications for research into areas such as infertility, reproductive medicine and rare genetic diseases.
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Affiliation(s)
- Kehui Xiang
- Howard Hughes Medical Institute, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, United States.,Whitehead Institute for Biomedical Research, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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Zhao LW, Fan HY. Revisiting poly(A)-binding proteins: Multifaceted regulators during gametogenesis and early embryogenesis. Bioessays 2021; 43:e2000335. [PMID: 33830517 DOI: 10.1002/bies.202000335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/27/2022]
Abstract
Post-transcriptional regulation faces a distinctive challenge in gametes. Transcription is limited when the germ cells enter the division phase due to condensed chromatin, while gene expression during gamete maturation, fertilization, and early cleavage depends on existing mRNA post-transcriptional coordination. The dynamics of the 3'-poly(A) tail play crucial roles in defining mRNA fate. The 3'-poly(A) tail is covered with poly(A)-binding proteins (PABPs) that help to mediate mRNA metabolism and recent work has shed light on the number and function of germ cell-specific expressed PABPs. There are two structurally different PABP groups distinguished by their cytoplasmic and nuclear localization. Both lack catalytic activity but are coupled with various roles through their interaction with multifunctional partners during mRNA metabolism. Here, we present a synopsis of PABP function during gametogenesis and early embryogenesis and describe both conventional and current models of the functions and regulation of PABPs, with an emphasis on the physiological significance of how germ cell-specific PABPs potentially affect human fertility.
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Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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31
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Sun J, Yang H, Yang X, Chen X, Xu H, Shen Y, Ding F, Gu X, Zhu J, Sun H. Global alternative splicing landscape of skeletal muscle atrophy induced by hindlimb unloading. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:643. [PMID: 33987341 PMCID: PMC8106077 DOI: 10.21037/atm-20-5388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background Long-term exposure to microgravity will cause skeletal muscle atrophy, which can cause serious harm to astronauts in space travel. Therefore, it is important to explore skeletal muscle atrophy’s molecular mechanism for its prevention and treatment. However, as an important regulatory approach of skeletal muscle physiology, the role of alternative splicing in skeletal muscle atrophy, especially skeletal muscle atrophy caused by disuse, is unclear. Methods We established a rat hindlimb unloading model and performed RNA sequencing on soleus muscle, which was seriously atrophied during unloading. Several bioinformatics methods were used to identify alternative splicing events and determine their gene functions. Results Many alternative splicing events were found to occur at different time points (12 h, 24 h, 36 h, 3 days, and 7 days) after hindlimb unloading. These differential alternative splicing events mainly occurred in the gene's coding domain sequence region, and 59% of the alternative splicing events caused open reading frameshift. Bioinformatics analysis results showed that genes with different alternative splicing events were enriched in multiple pathways related to muscle atrophy, including the insulin signaling pathway, endocytosis, mitophagy, and ubiquitin-proteasome pathway. Moreover, alternative splicing of several deubiquitinase genes persisted during skeletal muscle atrophy induced by unloading. Additionally, we identified 10 differentially expressed RNA binding proteins during skeletal muscle atrophy induced by unloading, mainly containing Xpo4, Eif4e2, P4ha1, Lrrfip1, Zc3h14, Emg1, Hnrnp h1, Mbnl2, RBfox1, and Mbnl1. Hnrnp h1 and Mbnl2 were significantly downregulated, and RBfox1 and Mbnl1 were significantly upregulated during skeletal muscle atrophy caused by unloading. Conclusions To the best of our knowledge, the present study is the first to propose alternative splicing alterations related to disuse-induced muscle atrophy, emphasizing that alternative splicing is a new focus of attention in the occurrence of muscle atrophy.
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Affiliation(s)
- Junjie Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Hua Yang
- Department of Neurosurgery, People's Hospital of Binhai County, Yancheng, China
| | - Xiaoming Yang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Xin Chen
- Department of Neurology, Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, China
| | - Hua Xu
- Department of Neurology, Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuntian Shen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Fei Ding
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Xiaosong Gu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Jianwei Zhu
- Department of Neurology, Department of Orthopedics, Affiliated Hospital of Nantong University, Nantong, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
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32
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Wu G, Schmid M, Rib L, Polak P, Meola N, Sandelin A, Jensen TH. A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome. Cell Rep 2021; 30:2387-2401.e5. [PMID: 32075771 DOI: 10.1016/j.celrep.2020.01.068] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/09/2019] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Degradation of transcripts in human nuclei is primarily facilitated by the RNA exosome. To obtain substrate specificity, the exosome is aided by adaptors; in the nucleoplasm, those adaptors are the nuclear exosome-targeting (NEXT) complex and the poly(A) (pA) exosome-targeting (PAXT) connection. How these adaptors guide exosome targeting remains enigmatic. Employing high-resolution 3' end sequencing, we demonstrate that NEXT substrates arise from heterogenous and predominantly pA- 3' ends often covering kilobase-wide genomic regions. In contrast, PAXT targets harbor well-defined pA+ 3' ends defined by canonical pA site use. Irrespective of this clear division, NEXT and PAXT act redundantly in two ways: (1) regional redundancy, where the majority of exosome-targeted transcription units produce NEXT- and PAXT-sensitive RNA isoforms, and (2) isoform redundancy, where the PAXT connection ensures fail-safe decay of post-transcriptionally polyadenylated NEXT targets. In conjunction, this provides a two-layered targeting mechanism for efficient nuclear sorting of the human transcriptome.
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Affiliation(s)
- Guifen Wu
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Leonor Rib
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Patrik Polak
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Nicola Meola
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark.
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Baker JD, Uhrich RL, Strovas TJ, Saxton AD, Kraemer BC. AlphaScreen Identifies MSUT2 Inhibitors for Tauopathy-Targeting Therapeutic Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:400-409. [PMID: 32981422 PMCID: PMC8592089 DOI: 10.1177/2472555220958387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tauopathies are neurological disorders characterized by intracellular tau deposits forming neurofibrillary tangles, neuropil threads, or other disease-specific aggregates composed of the protein tau. Tauopathy disorders include frontotemporal lobar degeneration, corticobasal degeneration, Pick's disease, and the largest cause of dementia, Alzheimer's disease. The lack of disease-modifying therapeutic strategies to address tauopathies remains a critical unmet need in dementia care. Thus, novel broad-spectrum tau-targeted therapeutics could have a profound impact in multiple tauopathy disorders, including Alzheimer's disease. Here we have designed a drug discovery paradigm to identify inhibitors of the pathological tau-enabling protein, MSUT2. We previously showed that activity of the RNA-binding protein MSUT2 drives tauopathy, including tau-mediated neurodegeneration and cognitive dysfunction, in mouse models. Thus, we hypothesized that MSUT2 inhibitors could be therapeutic for tauopathy disorders. Our pipeline for MSUT2 inhibitory compound identification included a primary AlphaScreen, followed by dose-response validation, a secondary fluorescence polarization orthogonal assay, a tertiary specificity screen, and a preliminary toxicity screen. Our work here serves as a proof-of-principle methodology for finding specific inhibitors of the poly(A) RNA-binding protein MSUT2 interaction. Here we identify 4,4'-diisothiocyanostilbene-2,2'-sulfonic acid (DIDS) as a potential tool compound for future work probing the mechanism of MSUT2-induced tau pathology.
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Affiliation(s)
- Jeremy D. Baker
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA
| | - Rikki L. Uhrich
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA
| | - Timothy J. Strovas
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA
| | - Aleen D. Saxton
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA
| | - Brian C. Kraemer
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
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Berman AJ, Thoreen CC, Dedeic Z, Chettle J, Roux PP, Blagden SP. Controversies around the function of LARP1. RNA Biol 2021; 18:207-217. [PMID: 32233986 PMCID: PMC7928164 DOI: 10.1080/15476286.2020.1733787] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
The RNA-binding protein LARP1 has generated interest in recent years for its role in the mTOR signalling cascade and its regulation of terminal oligopyrimidine (TOP) mRNA translation. Paradoxically, some scientists have shown that LARP1 represses TOP translation while others that LARP1 activates it. Here, we present opinions from four leading scientists in the field to discuss these and other contradictory findings.
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Affiliation(s)
- Andrea J. Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, USA
| | - Carson C. Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, USA
| | - Zinaida Dedeic
- Department of Oncology, University of Oxford, Oxford, UK
| | - James Chettle
- Department of Oncology, University of Oxford, Oxford, UK
| | - Philippe P. Roux
- Institute for Research in Immunology and Cancer (IRIC), Université De Montréal, Montreal, Quebec, Canada
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35
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Louis JM, Agarwal A, Aduri R, Talukdar I. Global analysis of RNA-protein interactions in TNF-α induced alternative splicing in metabolic disorders. FEBS Lett 2021; 595:476-490. [PMID: 33417721 DOI: 10.1002/1873-3468.14029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/26/2020] [Accepted: 12/10/2020] [Indexed: 12/27/2022]
Abstract
In this report, using the database of RNA-binding protein specificities (RBPDB) and our previously published RNA-seq data, we analyzed the interactions between RNA and RNA-binding proteins to decipher the role of alternative splicing in metabolic disorders induced by TNF-α. We identified 13 395 unique RNA-RBP interactions, including 385 unique RNA motifs and 35 RBPs, some of which (including MBNL-1 and 3, ZFP36, ZRANB2, and SNRPA) are transcriptionally regulated by TNF-α. In addition to some previously reported RBPs, such as RBMX and HuR/ELAVL1, we found a few novel RBPs, such as ZRANB2 and SNRPA, to be involved in the regulation of metabolic syndrome-associated genes that contain an enrichment of tetrameric RNA sequences (AUUU). Taken together, this study paves the way for novel RNA-protein interaction-based therapeutics for treating metabolic syndromes.
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Affiliation(s)
- Jiss Maria Louis
- Department of Biological Sciences, BITS Pilani, Zuarinagar, India
| | - Arjun Agarwal
- Department of Computer Science, BITS Pilani, Zuarinagar, India
| | - Raviprasad Aduri
- Department of Biological Sciences, BITS Pilani, Zuarinagar, India
| | - Indrani Talukdar
- Department of Biological Sciences, BITS Pilani, Zuarinagar, India
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36
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Torabi SF, Vaidya AT, Tycowski KT, DeGregorio SJ, Wang J, Shu MD, Steitz TA, Steitz JA. RNA stabilization by a poly(A) tail 3'-end binding pocket and other modes of poly(A)-RNA interaction. Science 2021; 371:science.abe6523. [PMID: 33414189 DOI: 10.1126/science.abe6523] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022]
Abstract
Polyadenylate [poly(A)] tail addition to the 3' end of a wide range of RNAs is a highly conserved modification that plays a central role in cellular RNA function. Elements for nuclear expression (ENEs) are cis-acting RNA elements that stabilize poly(A) tails by sequestering them in RNA triplex structures. A crystal structure of a double ENE from a rice hAT transposon messenger RNA complexed with poly(A)28 at a resolution of 2.89 angstroms reveals multiple modes of interaction with poly(A), including major-groove triple helices, extended minor-groove interactions with RNA double helices, a quintuple-base motif that transitions poly(A) from minor-groove associations to major-groove triple helices, and a poly(A) 3'-end binding pocket. Our findings both expand the repertoire of motifs involved in long-range RNA interactions and provide insights into how polyadenylation can protect an RNA's extreme 3' end.
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Affiliation(s)
- Seyed-Fakhreddin Torabi
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Anand T Vaidya
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.,TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Suzanne J DeGregorio
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Mei-Di Shu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA. .,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
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37
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Lehman BJ, Lopez-Diaz FJ, Santisakultarm TP, Fang L, Shokhirev MN, Diffenderfer KE, Manor U, Emerson BM. Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress. PLoS Genet 2021; 17:e1009277. [PMID: 33411704 PMCID: PMC7790283 DOI: 10.1371/journal.pgen.1009277] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 11/13/2020] [Indexed: 02/06/2023] Open
Abstract
The nuclear protein CCCTC-binding factor (CTCF) has diverse roles in chromatin architecture and gene regulation. Functionally, CTCF associates with thousands of genomic sites and interacts with proteins, such as cohesin, or non-coding RNAs to facilitate specific transcriptional programming. In this study, we examined CTCF during the cellular stress response in human primary cells using immune-blotting, quantitative real time-PCR, chromatin immunoprecipitation-sequence (ChIP-seq) analysis, mass spectrometry, RNA immunoprecipitation-sequence analysis (RIP-seq), and Airyscan confocal microscopy. Unexpectedly, we found that CTCF is exquisitely sensitive to diverse forms of stress in normal patient-derived human mammary epithelial cells (HMECs). In HMECs, a subset of CTCF protein forms complexes that localize to Serine/arginine-rich splicing factor (SC-35)-containing nuclear speckles. Upon stress, this species of CTCF protein is rapidly downregulated by changes in protein stability, resulting in loss of CTCF from SC-35 nuclear speckles and changes in CTCF-RNA interactions. Our ChIP-seq analysis indicated that CTCF binding to genomic DNA is largely unchanged. Restoration of the stress-sensitive pool of CTCF protein abundance and re-localization to nuclear speckles can be achieved by inhibition of proteasome-mediated degradation. Surprisingly, we observed the same characteristics of the stress response during neuronal differentiation of human pluripotent stem cells (hPSCs). CTCF forms stress-sensitive complexes that localize to SC-35 nuclear speckles during a specific stage of neuronal commitment/development but not in differentiated neurons. We speculate that these particular CTCF complexes serve a role in RNA processing that may be intimately linked with specific genes in the vicinity of nuclear speckles, potentially to maintain cells in a certain differentiation state, that is dynamically regulated by environmental signals. The stress-regulated activity of CTCF is uncoupled in persistently stressed, epigenetically re-programmed "variant" HMECs and certain cancer cell lines. These results reveal new insights into CTCF function in cell differentiation and the stress-response with implications for oxidative damage-induced cancer initiation and neuro-degenerative diseases.
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Affiliation(s)
- Bettina J. Lehman
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Fernando J. Lopez-Diaz
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Thom P. Santisakultarm
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Linjing Fang
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Maxim N. Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Kenneth E. Diffenderfer
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Uri Manor
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Beverly M. Emerson
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
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38
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Ustyantsev IG, Borodulina OR, Kramerov DA. Identification of nucleotide sequences and some proteins involved in polyadenylation of RNA transcribed by Pol III from SINEs. RNA Biol 2020; 18:1475-1488. [PMID: 33258402 DOI: 10.1080/15476286.2020.1857942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
We have previously reported that not only transcripts of RNA polymerase II (pol II), but also one type of RNA transcribed by RNA polymerase III (pol III), undergo AAUAAA-dependent polyadenylation. Such an unusual feature is inherent in Short Interspersed Elements (SINEs) from genomes of certain mammals. For polyadenylation of its transcript, SINE should contain, besides an AATAAA hexamer and a transcription terminator, two specific regions: β, located downstream of box B of a promoter, and τ, preceding AATAAA. Here, using nucleotide substitutions in SINEs B2 (mouse) and Ves (bat), we identified nucleotides of β regions necessary for polyadenylation of their transcripts. These sequences (β signals) are the following: ACCACATgg in B2 and GGGCATGT in Ves. Using this approach, we identified τ signal of SINE B2 (GCTACagTGTACTTACAT), where TGTA tetramer is most important for polyadenylation. In Ves, τ region is a long polypyrimidine motif which is able to interact with PTB protein in Ves transcripts. We demonstrated by knockdown that B2 and Ves transcript polyadenylation is performed by canonical poly(A) polymerase with the participation of proteins CSPF-160 and Fip1, the known factors of mRNA polyadenylation. We also showed that a factor CFIm partaking in polyadenylation of many mRNAs, is involved only in polyadenylation of B2 transcripts. CFIm seems to interact with τ signal of В2 RNA and thereby facilitates the recruiting of other proteins engaged in polyadenylation. Thus, SINEs utilize at least some proteins involved in polyadenylation of pol II transcripts to polyadenylate their pol III transcripts.
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Affiliation(s)
- Ilia G Ustyantsev
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga R Borodulina
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitri A Kramerov
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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39
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Baker JD, Uhrich RL, Strovas TJ, Saxton AD, Kraemer BC. Targeting Pathological Tau by Small Molecule Inhibition of the Poly(A):MSUT2 RNA-Protein Interaction. ACS Chem Neurosci 2020; 11:2277-2285. [PMID: 32589834 PMCID: PMC8629322 DOI: 10.1021/acschemneuro.0c00214] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Neurofibrillary tangles composed of aberrantly aggregating tau protein are a hallmark of Alzheimer's disease and related dementia disorders. Recent work has shown that mammalian suppressor of tauopathy 2 (MSUT2), also named ZC3H14 (Zinc Finger CCCH-Type Containing 14), controls accumulation of pathological tau in cultured human cells and mice. Knocking out MSUT2 protects neurons from neurodegenerative tauopathy and preserves learning and memory. MSUT2 protein functions to bind polyadenosine [poly(A)] tails of mRNA through its C-terminal CCCH type zinc finger domains, and loss of CCCH domain function suppresses tauopathy in Caenorhabditis elegans and mice. Thus, we hypothesized that inhibiting the poly(A):MSUT2 RNA-protein interaction would ameliorate pathological tau accumulation. Here we present a high-throughput screening method for the identification of small molecules inhibiting the poly(A):MSUT2 RNA-protein interaction. We employed a fluorescent polarization assay for initial small molecule discovery with the intention to repurpose hits identified from the NIH Clinical Collection (NIHCC). Our drug repurposing development workflow included validation of hits by dose-response analysis, specificity testing, orthogonal assays of activity, and cytotoxicity. Validated compounds passing through this screening funnel will be evaluated for translational effectiveness in future studies. This preclinical drug development pipeline identified diverse FDA approved drugs duloxetine, saquinavir, and clofazimine as potential repurposing candidates for reducing pathological tau accumulation.
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Affiliation(s)
- Jeremy D Baker
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, Washington 98104, United States
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108, United States
| | - Rikki L Uhrich
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108, United States
| | - Timothy J Strovas
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108, United States
| | - Aleen D Saxton
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108, United States
| | - Brian C Kraemer
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, Washington 98104, United States
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108, United States
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, United States
- Department of Pathology, University of Washington, Seattle, Washington 98195, United States
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40
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Zhao LW, Zhu YZ, Chen H, Wu YW, Pi SB, Chen L, Shen L, Fan HY. PABPN1L mediates cytoplasmic mRNA decay as a placeholder during the maternal-to-zygotic transition. EMBO Rep 2020; 21:e49956. [PMID: 32558204 DOI: 10.15252/embr.201949956] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Maternal mRNA degradation is a critical event of the maternal-to-zygotic transition (MZT) that determines the developmental potential of early embryos. Nuclear Poly(A)-binding proteins (PABPNs) are extensively involved in mRNA post-transcriptional regulation, but their function in the MZT has not been investigated. In this study, we find that the maternally expressed PABPN1-like (PABPN1L), rather than its ubiquitously expressed homolog PABPN1, acts as an mRNA-binding adapter of the mammalian MZT licensing factor BTG4, which mediates maternal mRNA clearance. Female Pabpn1l null mice produce morphologically normal oocytes but are infertile owing to early developmental arrest of the resultant embryos at the 1- to 2-cell stage. Deletion of Pabpn1l impairs the deadenylation and degradation of a subset of BTG4-targeted maternal mRNAs during the MZT. In addition to recruiting BTG4 to the mRNA 3'-poly(A) tails, PABPN1L is also required for BTG4 protein accumulation in maturing oocytes by protecting BTG4 from SCF-βTrCP1 E3 ubiquitin ligase-mediated polyubiquitination and degradation. This study highlights a noncanonical cytoplasmic function of nuclear poly(A)-binding protein in mRNA turnover, as well as its physiological importance during the MZT.
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Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Hao Chen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Shuai-Bo Pi
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lu Chen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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41
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He T, Wang M, Cheng A, Yang Q, Wu Y, Jia R, Liu M, Zhu D, Chen S, Zhang S, Zhao XX, Huang J, Sun D, Mao S, Ou X, Wang Y, Xu Z, Chen Z, Zhu L, Luo Q, Liu Y, Yu Y, Zhang L, Tian B, Pan L, Rehman MU, Chen X. Host shutoff activity of VHS and SOX-like proteins: role in viral survival and immune evasion. Virol J 2020; 17:68. [PMID: 32430029 PMCID: PMC7235440 DOI: 10.1186/s12985-020-01336-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/07/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Host shutoff refers to the widespread downregulation of host gene expression and has emerged as a key process that facilitates the reallocation of cellular resources for viral replication and evasion of host antiviral immune responses. MAIN BODY The Herpesviridae family uses a number of proteins that are responsible for host shutoff by directly targeting messenger RNA (mRNA), including virion host shutoff (VHS) protein and the immediate-early regulatory protein ICP27 of herpes simplex virus types 1 (HSV-1) and the SOX (shutoff and exonuclease) protein and its homologs in Gammaherpesvirinae subfamilies, although these proteins are not homologous. In this review, we highlight evidence that host shutoff is promoted by the VHS, ICP27 and SOX-like proteins and that they also contribute to immune evasion. CONCLUSIONS Further studies regarding the host shutoff proteins will not only contribute to provide new insights into the viral replication, expression and host immune evasion process, but also provide new molecular targets for the development of antiviral drugs and therapies.
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Affiliation(s)
- Tianqiong He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China. .,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Xin-Xin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Xuming Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Yin Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Zhiwen Xu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Zhengli Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Lin Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Qihui Luo
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Mujeeb Ur Rehman
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
| | - Xiaoyue Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan, 611130, People's Republic of China
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42
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Shukla TN, Song J, Campbell ZT. Molecular entrapment by RNA: an emerging tool for disrupting protein-RNA interactions in vivo. RNA Biol 2020; 17:417-424. [PMID: 31957541 PMCID: PMC7237136 DOI: 10.1080/15476286.2020.1717059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/09/2019] [Accepted: 01/12/2020] [Indexed: 10/25/2022] Open
Abstract
mRNA function is controlled by RNA-binding proteins. The specificity of RNA-binding factors for their targets is critical in that it enables all subsequent regulation. Despite widespread recognition of the pervasive role RNA-binding proteins play in development and disease, they remain challenging to target with small molecules. A renaissance in RNA therapeutics has led to the identification of modifications that substantially increase RNA stability. When combined with information regarding specificity, a new class of oligonucleotide mimics has emerged as a means to competitively disrupt the regulation of endogenous substrates. These decoys have been used to inhibit RNA-binding proteins in living animals. Decoys will likely provide new insights into the expansive roles of RNA-binding proteins in biology and disease. Here, we describe examples where they have been used and discuss how they could be applied to new targets.
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Affiliation(s)
- Tarjani N. Shukla
- The Department of Biological Sciences, University of Texas-Dallas, Richardson, TX, USA
| | - Jane Song
- The Department of Biological Sciences, University of Texas-Dallas, Richardson, TX, USA
| | - Zachary T. Campbell
- The Department of Biological Sciences, University of Texas-Dallas, Richardson, TX, USA
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43
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Zhang C, Cao P, Yang A, Xia X, Li Y, Shi M, Yang Y, Wei X, Yang C, Zhou G. Downregulation of ZC3H14 driven by chromosome 14q31 deletion promotes hepatocellular carcinoma progression by activating integrin signaling. Carcinogenesis 2020; 40:474-486. [PMID: 30371740 DOI: 10.1093/carcin/bgy146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 09/14/2018] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. Genomic copy number deletion at chromosome 14q31.1-32.13 was frequently observed in HCC; however, the relevant functional target(s) at that locus is not well determined. Here, we performed integrative genomic analyses and identified zinc finger CCCH-type containing 14 (ZC3H14) as a promising candidate at 14q31.1-32.13. We observed frequent copy number deletion (17.1%) and downregulation of ZC3H14 in primary HCC tissues. Downregulation of ZC3H14 was significantly associated with poor outcomes of patients with HCC. Overexpression of ZC3H14 in HCC cell lines significantly suppressed HCC cells growth in vitro and metastasis in vivo. In contrast, RNA interference silencing of ZC3H14 inhibited its tumor-suppressive function. Mechanismly, through combing bioinformatics analyses and experimental investigation, we demonstrated that loss of ZC3H14 promotes HCC progression through enhancing integrin pathway. This study suggests that ZC3H14 functions as a novel tumor suppressor and is a candidate prognostic biomarker for HCC patients.
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Affiliation(s)
- Chuxiao Zhang
- Affiliated Tumor Hospital of Guangxi Medical University, Nanning, P. R. China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Pengbo Cao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Aiqing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Xia Xia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Yuanfeng Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Mengting Shi
- Guangxi Medical University, Nanning, P. R. China
| | - Ying Yang
- Department of Radiation and Oncology, Navy General Hospital, Beijing, P. R. China
| | - Xiaojun Wei
- Department of Hepatobiliary Surgery, Aerospace Center Hospital, Beijing, P. R. China
| | - Chun Yang
- Affiliated Tumor Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,National Center for Protein Sciences at Beijing, Beijing, P. R. China.,Guangxi Medical University, Nanning, P. R. China
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44
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Chung HW, Weng JC, King CE, Chuang CF, Chow WY, Chang YC. BDNF elevates the axonal levels of hnRNPs Q and R in cultured rat cortical neurons. Mol Cell Neurosci 2019; 98:97-108. [PMID: 31202892 DOI: 10.1016/j.mcn.2019.06.005] [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: 11/01/2018] [Revised: 05/08/2019] [Accepted: 06/12/2019] [Indexed: 11/17/2022] Open
Abstract
Local translation plays important roles in the maintenance and various functions of axons, and dysfunctions of local translation in axons are implicated in various neurological diseases. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are RNA binding proteins with multiple functions in RNA metabolism. Here, we identified 20 hnRNPs in the axons of cultured rat cortical neurons by interrogating published axon mass spectrometric databases with rat protein databases. Among those identified in axons are highly related hnRNPs Q and R. RT-PCR analysis indicated that axons also contained low levels of hnRNPs Q and R mRNAs. We further found that BDNF treatments raised the levels of hnRNPs Q and R proteins in whole neurons and axons. BDNF also increased the level of poly(A) RNA as well as the proportion of poly(A) RNA granules containing hnRNPs Q and R in the axon. However, following severing the connection between the cell bodies and axons, BDNF did not affect the levels of hnRNPs Q and R, the content of poly(A) RNA, or the colocalization of poly(A) RNA and hnRNPs Q and R in the axon any more, although BDNF still stimulated the local translation in severed axons as it did in intact axons. The results are consistent with that BDNF enhances the axonal transport of RNA granules. The results further suggest that hnRNPs Q and R play a role in the mechanism underlying the enhancement of axonal RNA transport by BDNF.
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Affiliation(s)
- Hui-Wen Chung
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan.
| | - Ju-Chen Weng
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-En King
- Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Fan Chuang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan.
| | - Wei-Yuan Chow
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.
| | - Yen-Chung Chang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan; Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan.
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45
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Translational Control of Canonical and Non-Canonical Translation Initiation Factors at the Sea Urchin Egg to Embryo Transition. Int J Mol Sci 2019; 20:ijms20030626. [PMID: 30717141 PMCID: PMC6387300 DOI: 10.3390/ijms20030626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 02/06/2023] Open
Abstract
Sea urchin early development is a powerful model to study translational regulation under physiological conditions. Fertilization triggers an activation of the translation machinery responsible for the increase of protein synthesis necessary for the completion of the first embryonic cell cycles. The cap-binding protein eIF4E, the helicase eIF4A and the large scaffolding protein eIF4G are assembled upon fertilization to form an initiation complex on mRNAs involved in cap-dependent translation initiation. The presence of these proteins in unfertilized and fertilized eggs has already been demonstrated, however data concerning the translational status of translation factors are still scarce. Using polysome fractionation, we analyzed the impact of fertilization on the recruitment of mRNAs encoding initiation factors. Strikingly, whereas the mRNAs coding eIF4E, eIF4A, and eIF4G were not recruited into polysomes at 1 h post-fertilization, mRNAs for eIF4B and for non-canonical initiation factors such as DAP5, eIF4E2, eIF4E3, or hnRNP Q, are recruited and are differentially sensitive to the activation state of the mechanistic target of rapamycin (mTOR) pathway. We discuss our results suggesting alternative translation initiation in the context of the early development of sea urchins.
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46
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Diamos AG, Mason HS. Chimeric 3' flanking regions strongly enhance gene expression in plants. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1971-1982. [PMID: 29637682 PMCID: PMC6230951 DOI: 10.1111/pbi.12931] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/07/2018] [Accepted: 03/30/2018] [Indexed: 05/24/2023]
Abstract
Plants represent a promising platform for the highly scalable production of recombinant proteins. Previously, we identified the tobacco extensin terminator lacking its intron as an element that reduced transcript read-through and improved recombinant protein production in a plant-based system. In this study, we systematically compared nonreplicating plant expression vectors containing over 20 commonly used or newly identified terminators from diverse sources. We found that eight gene terminators enhance reporter gene expression significantly more than the commonly used 35S and NOS terminators. The intronless extensin terminator provided a 13.6-fold increase compared with the NOS terminator. Combining terminators in tandem produced large synergistic effects, with many combinations providing a >25-fold increase in expression. Addition of the tobacco Rb7 or TM6 matrix attachment region (MAR) strongly enhanced protein production when added to most terminators, with the Rb7 MAR providing the greatest enhancement. Using deletion analysis, the full activity of the 1193 bp Rb7 MAR was found to require only a 463-bp region at its 3' end. Combined terminators and MAR together provided a >60-fold increase compared with the NOS terminator alone. These combinations were then placed in a replicating geminiviral vector, providing a total of >150-fold enhancement over the original NOS vector, corresponding to an estimated yield of 3-5 g recombinant protein per kg leaf fresh weight or around 50% of the leaf total soluble protein. These results demonstrate the importance of 3' flanking regions in optimizing gene expression and show great potential for 3' flanking regions to improve DNA-based recombinant protein production systems.
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Affiliation(s)
- Andrew G. Diamos
- Center for Immunotherapy, Vaccines and VirotherapyBiodesign Institute at ASU, and School of Life SciencesArizona State UniversityTempeAZUSA
| | - Hugh S. Mason
- Center for Immunotherapy, Vaccines and VirotherapyBiodesign Institute at ASU, and School of Life SciencesArizona State UniversityTempeAZUSA
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Nicholson AL, Pasquinelli AE. Tales of Detailed Poly(A) Tails. Trends Cell Biol 2018; 29:191-200. [PMID: 30503240 DOI: 10.1016/j.tcb.2018.11.002] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 11/18/2022]
Abstract
Poly(A) tails are non-templated additions of adenosines at the 3' ends of most eukaryotic mRNAs. In the nucleus, these RNAs are co-transcriptionally cleaved at a poly(A) site and then polyadenylated before being exported to the cytoplasm. In the cytoplasm, poly(A) tails play pivotal roles in the translation and stability of the mRNA. One challenge in studying poly(A) tails is that they are difficult to sequence and accurately measure. However, recent advances in sequencing technology, computational algorithms, and other assays have enabled a more detailed look at poly(A) tail length genome-wide throughout many developmental stages and organisms. With the help of these advances, our understanding of poly(A) tail length has evolved over the past 5 years with the recognition that highly expressed genes can have short poly(A) tails and the elucidation of the seemingly contradictory roles for poly(A)-binding protein (PABP) in facilitating both protection and deadenylation.
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Affiliation(s)
- Angela L Nicholson
- Division of Biology, University of California, San Diego (USCD), La Jolla, CA 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego (USCD), La Jolla, CA 92093-0349, USA.
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48
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn 2018; 37:2837-2866. [PMID: 30052138 DOI: 10.1080/07391102.2018.1503972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
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Affiliation(s)
- Margarita I Zarudnaya
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Iryna M Kolomiets
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Andriy L Potyahaylo
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv , Ukraine
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Tudek A, Lloret-Llinares M, Jensen TH. The multitasking polyA tail: nuclear RNA maturation, degradation and export. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0169. [PMID: 30397105 DOI: 10.1098/rstb.2018.0169] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
A polyA (pA) tail is an essential modification added to the 3' ends of a wide range of RNAs at different stages of their metabolism. Here, we describe the main sources of polyadenylation and outline their underlying biochemical interactions within the nuclei of budding yeast Saccharomyces cerevisiae, human cells and, when relevant, the fission yeast Schizosaccharomyces pombe Polyadenylation mediated by the S. cerevisiae Trf4/5 enzymes, and their human homologues PAPD5/7, typically leads to the 3'-end trimming or complete decay of non-coding RNAs. By contrast, the primary function of canonical pA polymerases (PAPs) is to produce stable and nuclear export-competent mRNAs. However, this dichotomy is becoming increasingly blurred, at least in S. pombe and human cells, where polyadenylation mediated by canonical PAPs may also result in transcript decay.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark
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The EGF/hnRNP Q1 axis is involved in tumorigenesis via the regulation of cell cycle-related genes. Exp Mol Med 2018; 50:1-14. [PMID: 29884818 PMCID: PMC5994831 DOI: 10.1038/s12276-018-0101-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 01/10/2023] Open
Abstract
Heterogeneous nuclear ribonucleoprotein (hnRNP) Q1, an RNA-binding protein, has been implicated in many post-transcriptional processes, including RNA metabolism and mRNA splicing and translation. However, the role of hnRNP Q1 in tumorigenesis remains unclear. We previously performed RNA immunoprecipitation (RIP)-seq analysis to identify hnRNP Q1-interacting mRNAs and found that hnRNP Q1 targets a group of genes that are involved in mitotic regulation, including Aurora-A. Here, we demonstrate that altering the hnRNP Q1 level influences the expression of the Aurora-A protein, but not its mRNA. Stimulation with epidermal growth factor (EGF) enhances both binding between hnRNP Q1 and Aurora-A mRNA as well as the efficacy of the hnRNP Q1-induced translation of Aurora-A mRNA. The EGF/hnRNP Q1-induced translation of Aurora-A mRNA is mediated by the mTOR and ERK pathways. In addition, we show that hnRNP Q1 up-regulates the translation of a group of spindle assembly checkpoint (SAC) genes. hnRNP Q1 overexpression is positively correlated with the levels of Aurora-A and the SAC genes in human colorectal cancer tissues. In summary, our data suggest that hnRNP Q1 plays an important role in regulating the expression of a group of cell cycle-related genes. Therefore, it may contribute to tumorigenesis by up-regulating the translation of these genes in colorectal cancer. An RNA-binding protein contributes to cancer by boosting the protein-making potential of various genes involved in the cell cycle and cell division. Researchers in Taiwan led by Liang-Yi Hung from the National Cheng Kung University in Tainan, Taiwan, previously showed that a cancer-causing protein implicated in tumors of the colon and elsewhere gets induced by both an RNA-binding protein called hnRNP Q1 and a growth factor called EGF. Now, they have demonstrated that these two molecules work in concert to boost the efficiency by which the RNA encoding the cancer-causing protein gets translated into the protein. They also showed that hnRNP Q1 serves a similar RNA-modulating function for several genes involved in spindle checkpoint during cell division. Together, the findings point to hnRNP Q1 as a potential target for future anti-cancer drugs.
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