1
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Wang F, Fan Y, Li Y, Zhou Y, Wang X, Zhu M, Chen X, Xue Y, Shen C. Identification of differentially expressed genes of blood leukocytes for Schizophrenia. Front Genet 2024; 15:1398240. [PMID: 38988837 PMCID: PMC11233772 DOI: 10.3389/fgene.2024.1398240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Background Schizophrenia (SCZ) is a severe neurodevelopmental disorder with brain dysfunction. This study aimed to use bioinformatic analysis to identify candidate blood biomarkers for SCZ. Methods The study collected peripheral blood leukocyte samples of 9 SCZ patients and 20 healthy controls for RNA sequencing analysis. Bioinformatic analyses included differentially expressed genes (DEGs) analysis, pathway enrichment analysis, and weighted gene co-expression network analysis (WGCNA). Results This study identified 1,205 statistically significant DEGs, of which 623 genes were upregulated and 582 genes were downregulated. Functional enrichment analysis showed that DEGs were mainly enriched in cell chemotaxis, cell surface, and serine peptidase activity, as well as involved in Natural killer cell-mediated cytotoxicity. WGCNA identified 16 gene co-expression modules, and five modules were significantly correlated with SCZ (p < 0.05). There were 106 upregulated genes and 90 downregulated genes in the five modules. The top ten genes sorted by the Degree algorithm were RPS28, BRD4, FUS, PABPC1, PCBP1, PCBP2, RPL27A, RPS21, RAG1, and RPL27. RAG1 and the other nine genes belonged to the turquoise and pink module respectively. Pathway enrichment analysis indicated that these 10 genes were mainly involved in processes such as Ribosome, cytoplasmic translation, RNA binding, and protein binding. Conclusion This study finds that the gene functions in key modules and related enrichment pathways may help to elucidate the molecular pathogenesis of SCZ, and the potential of key genes to become blood biomarkers for SCZ warrants further validation.
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Affiliation(s)
- Feifan Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yao Fan
- Department of Clinical Epidemiology, Jiangsu Province Geriatric Institute, Geriatric Hospital of Nanjing Medical University, Nanjing, China
| | - Yinghui Li
- Department of Medical Psychology, Huai'an Third Hospital, Huai'an, China
| | - Yuan Zhou
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xin Wang
- Department of Medical Laboratory, Huai'an Third Hospital, Huai'an, China
| | - Mengya Zhu
- Department of Medical Laboratory, Huai'an Third Hospital, Huai'an, China
| | - Xuefei Chen
- Department of Medical Laboratory, Huai'an Third Hospital, Huai'an, China
| | - Yong Xue
- Department of Medical Laboratory, Huai'an Third Hospital, Huai'an, China
| | - Chong Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
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2
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Lo R, Gonçalves-Carneiro D. Sensing nucleotide composition in virus RNA. Biosci Rep 2023; 43:BSR20230372. [PMID: 37606964 PMCID: PMC10500230 DOI: 10.1042/bsr20230372] [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: 06/13/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 08/23/2023] Open
Abstract
Nucleotide composition plays a crucial role in the structure, function and recognition of RNA molecules. During infection, virus RNA is exposed to multiple endogenous proteins that detect local or global compositional biases and interfere with virus replication. Recent advancements in RNA:protein mapping technologies have enabled the identification of general RNA-binding preferences in the human proteome at basal level and in the context of virus infection. In this review, we explore how cellular proteins recognise nucleotide composition in virus RNA and the impact these interactions have on virus replication. Protein-binding G-rich and C-rich sequences are common examples of how host factors detect and limit infection, and, in contrast, viruses may have evolved to purge their genomes from such motifs. We also give examples of how human RNA-binding proteins inhibit virus replication, not only by destabilising virus RNA, but also by interfering with viral protein translation and genome encapsidation. Understanding the interplay between cellular proteins and virus RNA composition can provide insights into host-virus interactions and uncover potential targets for antiviral strategies.
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Affiliation(s)
- Raymon Lo
- Imperial College London, Department of Infectious Disease, Imperial College London, London, U.K
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3
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Yang B, Wu Y, Chen Y, Li Y, Wang J, Cha X, Liu J. MiR-5195-3p targets the PCBP2/PI3K/AKT pathway to inhibit melanoma cell proliferation and migration. Heliyon 2023; 9:e19227. [PMID: 37662755 PMCID: PMC10474410 DOI: 10.1016/j.heliyon.2023.e19227] [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: 03/16/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Although miR-5195-3p has been acknowledged for its tumor suppressor role in diverse cancer categories, its precise functions and mechanisms concerning melanoma have not been comprehensively elucidated. In this study, we employed quantitative reverse transcription PCR, Western blot analysis, and immunohistochemistry staining to investigate the expression patterns of miR-5195-3p and poly (rC) binding protein 2 (PCBP2) in melanoma tissues compared to adjacent tissues. Our findings revealed downregulation of miR-5195-3p and upregulation of PCBP2 in melanoma tissues. Through the implementation of a luciferase reporter assay, we successfully identified PCBP2 as a newly discovered target of miR-5195-3p in melanoma cells. Enforced expression of miR-5195-3p via mimics inhibited cell proliferation and migration in A375 and A2058 cells, as demonstrated by CCK-8 and transwell migration assays. In melanoma cells, reintroduction of PCBP2 partially reversed the inhibitory effects of miR-5195-3p overexpression. Treatment with LY294002, an inhibitor of the PI3K/AKT signaling pathway, also reversed the effects of PCBP2 in melanoma cells. Furthermore, our results suggest that miR-5195-3p inhibits the activation of the PI3K/AKT signaling pathway in melanoma by inhibiting PCBP2. In conclusion, our research has identified the miR-5195-3p targeting of the PCBP2-mediated PI3K/AKT signaling pathway as a potential therapeutic target for melanoma treatment.
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Affiliation(s)
- Botao Yang
- Department of Dermatology, The First Affiliated Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
- Department of Dermatology, Guangdong Provincial People's Hospital's Nanhai Hospital, Foshan, Guangdong Province, China
| | - Yucai Wu
- Department of Dermatology, Guangdong Provincial People's Hospital's Nanhai Hospital, Foshan, Guangdong Province, China
| | - Yang Chen
- Department of Dermatology, Yangjiang People's Hospital, Yangjiang, Guangdong Province, China
| | - Yongshuang Li
- Department of Dermatology, The Third People's Hospital of Shenzhen, Shenzhen, Guangdong Province, China
| | - Jinhua Wang
- Department of Dermatology, The Affiliated Shunde Hospital of Jinan University, Foshan City, Guangdong Province, China
| | - Xushan Cha
- Department of Dermatology, The First Affiliated Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Jing Liu
- Department of Dermatology, The First Affiliated Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
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4
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Tamás V, Righi C, Mészáros I, D'Errico F, Olasz F, Casciari C, Zádori Z, Magyar T, Petrini S, Feliziani F. Involvement of the MGF 110-11L Gene in the African Swine Fever Replication and Virulence. Vaccines (Basel) 2023; 11:vaccines11040846. [PMID: 37112759 PMCID: PMC10145817 DOI: 10.3390/vaccines11040846] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
African swine fever (ASF) is a highly lethal hemorrhagic viral disease that causes extensive economic and animal welfare losses in the Eurasian pig (Sus scrofa) population. To date, no effective and safe vaccines have been marketed against ASF. A starting point for vaccine development is using naturally occurring attenuated strains as a vaccine base. Here, we aimed to remove the multigene family (MGF) 110 gene of unknown function from the Lv17/WB/Rie1 genome to improve the usability of the virus as a live-attenuated vaccine, reducing unwanted side effects. The MGF 110-11L gene was deleted using the CRISPR/Cas9 method, and the safety and efficacy of the virus were tested in pigs after isolation. The vaccine candidates administered at high doses showed reduced pathogenicity compared to the parental strain and induced immunity in vaccinated animals, although several mild clinical signs were observed. Although Lv17/WB/Rie1/d110-11L cannot be used as a vaccine in its current form, it was encouraging that the undesirable side effects of Lv17/WB/Rie1 at high doses can be reduced by additional mutations without a significant reduction in its protective capacity.
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Affiliation(s)
- Vivien Tamás
- Institute for Veterinary Medical Research, Hungária krt. 21, 1143 Budapest, Hungary
| | - Cecilia Righi
- Istituto Zooprofilattico Sperimentale Umbria-Marche "Togo Rosati", Via Gaetano Salvemini, 1, 06126 Perugia, Italy
| | - István Mészáros
- Institute for Veterinary Medical Research, Hungária krt. 21, 1143 Budapest, Hungary
| | - Federica D'Errico
- Istituto Zooprofilattico Sperimentale Umbria-Marche "Togo Rosati", Via Gaetano Salvemini, 1, 06126 Perugia, Italy
| | - Ferenc Olasz
- Institute for Veterinary Medical Research, Hungária krt. 21, 1143 Budapest, Hungary
| | - Cristina Casciari
- Istituto Zooprofilattico Sperimentale Umbria-Marche "Togo Rosati", Via Gaetano Salvemini, 1, 06126 Perugia, Italy
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Hungária krt. 21, 1143 Budapest, Hungary
| | - Tibor Magyar
- Institute for Veterinary Medical Research, Hungária krt. 21, 1143 Budapest, Hungary
| | - Stefano Petrini
- Istituto Zooprofilattico Sperimentale Umbria-Marche "Togo Rosati", Via Gaetano Salvemini, 1, 06126 Perugia, Italy
| | - Francesco Feliziani
- Istituto Zooprofilattico Sperimentale Umbria-Marche "Togo Rosati", Via Gaetano Salvemini, 1, 06126 Perugia, Italy
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5
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Lyu Y, Song L, Mao R, Liu C, Feng M, Wu C, Pei R, Ding L, Wang J. hnRNP K induces HPV16 oncogene expression and promotes cervical cancerization. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04585-6. [PMID: 36700980 DOI: 10.1007/s00432-023-04585-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
PURPOSE This study aims to explore the expression of hnRNP K in cervical carcinogenesis and to investigate the regulatory role of hnRNP K on HPV16 oncogene expression as well as biological changes in cervical cancer cells. METHODS In total 1042 subjects, including 573 with the normal cervix and 469 with different grades of cervical lesions were enrolled in this study to explore the association between hnRNP K and HPV16 oncogene expression in cervical carcinogenesis. Additionally, the Gene Omnibus (GEO) database was used to analyze hnRNP K mRNA expression in cervical cancerization. Meanwhile, the effects of hnRNP K on cell biological functions and HPV16 oncogene expression were investigated in Siha cells. Moreover, Function analyses were conducted using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases after ChIP-seq. RESULTS hnRNP K was highly expressed in cervical cancer and precancerous lesions, and positively correlated with HPV16 E6, but negatively correlated with HPV16 E2 and HPV16 E2/E6 ratio. hnRNP K induced cell proliferation, inhibited apoptosis and caused cell cycle arrest in the S phase, and particularly increased HPV16 E6 protein expression. CONCLUSION This study revealed that hnRNP K overexpression has important warning significance for the malignant transformation of cervical lesions, and could be used as a potential therapeutic target for inhibiting the carcinogenicity of HPV16 and prevention of cervical carcinogenesis.
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Affiliation(s)
- Yuanjing Lyu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Li Song
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Rui Mao
- Questrom School of Business, Boston University, Boston, MA, USA
| | - Chunliang Liu
- Department of Gastroenterology, Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Meijuan Feng
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Caihong Wu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Ruixin Pei
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Ling Ding
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Jintao Wang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China.
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6
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Iwai M, Kajino T, Nakatochi M, Yanagisawa K, Hosono Y, Isomura H, Shimada Y, Suzuki M, Taguchi A, Takahashi T. Long non-coding RNA TILR constitutively represses TP53 and apoptosis in lung cancer. Oncogene 2023; 42:364-373. [PMID: 36522487 DOI: 10.1038/s41388-022-02546-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 12/16/2022]
Abstract
Non-coding RNAs have an integral regulatory role in numerous functions related to lung cancer development. Here, we report identification of a novel lncRNA, termed TP53-inhibiting lncRNA (TILR), which was found to function as a constitutive negative regulator of p53 expression, including activation of downstream genes such as p21 and MDM2, and induction of apoptosis. A proteomic search for TILR-associated proteins revealed an association with PCBP2, while the mid-portion of TILR was found to be required for both PCBP2 and p53 mRNA binding. In addition, depletion of PCBP2 resulted in phenocopied effects of TILR silencing. TILR was also shown to suppress p53 expression in a post-transcriptional manner, as well as via a positive feedback loop involving p53 and Fanconi anemia pathway genes. Taken together, the present findings clearly demonstrate that TILR constitutively inhibits p53 expression in cooperation with PCBP2, thus maintaining p53 transcriptional activity at a level sufficiently low for avoidance of spurious apoptosis induction.
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Affiliation(s)
- Mika Iwai
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Taisuke Kajino
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, 461-8673, Japan
| | - Kiyoshi Yanagisawa
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Department of Molecular and Cancer Medicine, Faculty of Pharmacy, Meijo University, Nagoya, 468-8502, Japan
| | - Yasuyuki Hosono
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan.,Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Hisanori Isomura
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
| | - Yukako Shimada
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
| | - Motoshi Suzuki
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Department of Molecular Oncology, School of Medicine, Fujita Health University, Toyoake, 470-1192, Japan
| | - Ayumu Taguchi
- Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan.,Division of Advanced Cancer Diagnostics, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, 464-8681, Japan
| | - Takashi Takahashi
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan. .,Aichi Cancer Center, Nagoya, 464-8681, Japan.
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7
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Arora EK, Sharma V. Iron metabolism: pathways and proteins in homeostasis. REV INORG CHEM 2022. [DOI: 10.1515/revic-2022-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Iron is essential to human survival. The biological role and trafficking of this trace essential inorganic element which is also a potential toxin is constantly being researched and unfolded. Vital for oxygen transport, DNA synthesis, electron transport, neurotransmitter biosynthesis and present in numerous other heme and non-heme enzymes the physiological roles are immense. Understanding the molecules and pathways that regulate this essential element at systemic and cellular levels are of importance in improving therapeutic strategies for iron related disorders. This review highlights the progress in understanding the metabolism and trafficking of iron along with the pathophysiology of iron related disorders.
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Affiliation(s)
- Ekta Kundra Arora
- Chemistry Department, St. Stephen’s College , University of Delhi , Delhi 110007 , India
| | - Vibha Sharma
- Chemistry Department, St. Stephen’s College , University of Delhi , Delhi 110007 , India
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8
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Generation of PCBP1-deficient pigs using CRISPR/Cas9-mediated gene editing. iScience 2022; 25:105268. [PMID: 36274935 PMCID: PMC9579030 DOI: 10.1016/j.isci.2022.105268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/16/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
Classical swine fever virus (CSFV), a classic swine fever pathogen, causes severe economic losses worldwide. Poly (rC)-binding protein 1 (PCBP1), which interacts with Npro of CSFV, plays a vital role in CSFV growth. We are the first to report the generation of PCBP1-deficient pigs via gene-editing technology. The PCBP1-deficient pigs exhibited normal birth weight and reproductive-performance traits and developed normally. Viral challenge experiments indicated that primary cells isolated from F0- and F1-generation pigs exhibited significantly reduced CSFV infection. Additional mechanistic exploration further confirmed that the PCBP1 deficiency-mediated antiviral effect is related to the activation of type I interferon (IFN). Besides showing that a gene-editing strategy could be used to generate PCBP1-deficient pigs, our study introduces a valuable animal model for further investigating the infection mechanisms of CSFV that will help to develop better antiviral solutions. Reduced CSFV infection in PCBP1-deficient cells is related to activated ISGs expression PCBP1-deficient pigs were successfully generated via gene-editing technology Primary cells isolated from PCBP1-deficient pigs exhibited reduced CSFV infection
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9
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Structural Characteristics of the 5′-Terminal Region of Mouse p53 mRNA and Identification of Proteins That Bind to This mRNA Region. Int J Mol Sci 2022; 23:ijms23179709. [PMID: 36077109 PMCID: PMC9456389 DOI: 10.3390/ijms23179709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 12/15/2022] Open
Abstract
A mouse model has often been used in studies of p53 gene expression. Detailed interpretation of functional studies is, however, hampered by insufficient knowledge of the impact of mouse p53 mRNA’s structure and its interactions with proteins in the translation process. In particular, the 5′-terminal region of mouse p53 mRNA is an important region which takes part in the regulation of the synthesis of p53 protein and its N-truncated isoform Δ41p53. In this work, the spatial folding of the 5′-terminal region of mouse p53 mRNA and its selected sub-fragments was proposed based on the results of the SAXS method and the RNAComposer program. Subsequently, RNA-assisted affinity chromatography was used to identify proteins present in mouse fibroblast cell lysates that are able to bind the RNA oligomer, which corresponds to the 5′-terminal region of mouse p53 mRNA. Possible sites to which the selected, identified proteins can bind were proposed. Interestingly, most of these binding sites coincide with the sites determined as accessible to hybridization of complementary oligonucleotides. Finally, the high binding affinity of hnRNP K and PCBP2 to the 5′-terminal region of mouse p53 mRNA was confirmed and their possible binding sites were proposed.
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10
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Duan L, Zaepfel BL, Aksenova V, Dasso M, Rothstein JD, Kalab P, Hayes LR. Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export. Cell Rep 2022; 40:111106. [PMID: 35858577 PMCID: PMC9345261 DOI: 10.1016/j.celrep.2022.111106] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 03/26/2022] [Accepted: 06/27/2022] [Indexed: 11/27/2022] Open
Abstract
Nuclear clearance of the RNA-binding protein TDP-43 is a hallmark of neurodegeneration and an important therapeutic target. Our current understanding of TDP-43 nucleocytoplasmic transport does not fully explain its predominantly nuclear localization or mislocalization in disease. Here, we show that TDP-43 exits nuclei by passive diffusion, independent of facilitated mRNA export. RNA polymerase II blockade and RNase treatment induce TDP-43 nuclear efflux, suggesting that nuclear RNAs sequester TDP-43 in nuclei and limit its availability for passive export. Induction of TDP-43 nuclear efflux by short, GU-rich oligomers (presumably by outcompeting TDP-43 binding to endogenous nuclear RNAs), and nuclear retention conferred by splicing inhibition, demonstrate that nuclear TDP-43 localization depends on binding to GU-rich nuclear RNAs. Indeed, RNA-binding domain mutations markedly reduce TDP-43 nuclear localization and abolish transcription blockade-induced nuclear efflux. Thus, the nuclear abundance of GU-RNAs, dictated by the balance of transcription, pre-mRNA processing, and RNA export, regulates TDP-43 nuclear localization.
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Affiliation(s)
- Lauren Duan
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Benjamin L Zaepfel
- Biochemistry, Cellular and Molecular Biology Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Petr Kalab
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Lindsey R Hayes
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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11
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Poly(rC) binding protein 1 benefits coxsackievirus B3 infection via suppressing the translation of p62/SQSTM1. Virus Res 2022; 318:198851. [PMID: 35764193 DOI: 10.1016/j.virusres.2022.198851] [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: 11/14/2021] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022]
Abstract
Coxsackievirus B3 (CVB3) is a positive single-strand RNA virus causing myocarditis, pancreatitis and meningitis. During CVB3 infection, various host cellular components, including proteins and non-coding RNAs, interact with the virus and affect viral infection. Poly(rC) binding protein 1 (PCBP1) is a multifunctional RNA binding protein regulating transcription, translation and mRNA stability of a variety of genes. In this study, we observed a significant reduction of PCBP1 protein during CVB3 infection. By bioinformatic prediction and luciferase-assay verification, we confirmed that the expression of PCBP1 was directly inhibited by miR-21, a microRNA upregulated during CVB3 infection. Furthermore, we found that overexpression of PCBP1 promoted CVB3 infection and knocking down of PCBP1 inhibited it. In the subsequent mechanism study, our results revealed that PCBP1 blocked the translation of p62/SQSTM1 (sequestosome 1), an autophagy-receptor protein suppressing CVB3 replication, by interacting with the cis-element in the 5' untranslational region (5' UTR) of p62/SQSTM1. In summary, our studies have identified PCBP1 as a beneficial factor for CVB3 infection. These findings may deepen the understanding of host-virus interactions and provide a potential target for intervention of CVB3 infection.
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12
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Zhao H, Wei Z, Shen G, Chen Y, Hao X, Li S, Wang R. Poly(rC)-binding proteins as pleiotropic regulators in hematopoiesis and hematological malignancy. Front Oncol 2022; 12:1045797. [PMID: 36452487 PMCID: PMC9701828 DOI: 10.3389/fonc.2022.1045797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Poly(rC)-binding proteins (PCBPs), a defined subfamily of RNA binding proteins, are characterized by their high affinity and sequence-specific interaction with poly-cytosine (poly-C). The PCBP family comprises five members, including hnRNP K and PCBP1-4. These proteins share a relatively similar structure motif, with triple hnRNP K homology (KH) domains responsible for recognizing and combining C-rich regions of mRNA and single- and double-stranded DNA. Numerous studies have indicated that PCBPs play a prominent role in hematopoietic cell growth, differentiation, and tumorigenesis at multiple levels of regulation. Herein, we summarized the currently available literature regarding the structural and functional divergence of various PCBP family members. Furthermore, we focused on their roles in normal hematopoiesis, particularly in erythropoiesis. More importantly, we also discussed and highlighted their involvement in carcinogenesis, including leukemia and lymphoma, aiming to clarify the pleiotropic roles and molecular mechanisms in the hematopoietic compartment.
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Affiliation(s)
- Huijuan Zhao
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Ziqing Wei
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Guomin Shen
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Yixiang Chen
- Henan International Joint Laboratory of Thrombosis and Hemostasis, Henan University of Science and Technology, Luoyang, China.,Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Xueqin Hao
- Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Sanqiang Li
- Basic Medical College, Henan University of Science and Technology, Luoyang, China
| | - Rong Wang
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
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13
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Cellular hnRNPAB interacts with avian influenza viral protein PB2 and inhibits virus replication potentially by restricting PB2 mRNA nuclear export and PB2 protein level. Virus Res 2021; 305:198573. [PMID: 34555436 DOI: 10.1016/j.virusres.2021.198573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 11/24/2022]
Abstract
The PB2 protein of avian influenza virus (AIV) is essential for transcription and replication of virus genome. In this study, we reported that chicken heterogenous nuclear riboncleoprotein AB (hnRNPAB) cooperated with avian influenza viral protein PB2 and inhibited the polymerase activity and virus replication. We found that hnRNPAB was associated with PB2 mRNA and overexpression of hnRNPAB reduced PB2 mRNA nuclear export and PB2 protein level, but had no influence on PB2 mRNA level. At the same time, overexpression of hnRNPAB also reduced protein levels rather than mRNA levels of PA, PB1 and NP. In addition, overexpression of hnRNPAB restricted the polymerase activity and virus replication, while knockdown of hnRNPAB resulted in enhanced polymerase activity and virus replication. Lastly, virus infection induced the nuclear accumulation of hnRNPAB, but did not cause the change of expression level of endogenous hnRNPAB in DF-1 cells. Collectively, these findings suggested that hnRNPAB played a restrictive role in polymerase activity and virus replication potentially through inhibiting PB2 mRNA nuclear export and PB2 protein level.
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14
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Singh CK, Singh D, Taunk J, Chaudhary P, Tomar RSS, Chandra S, Singh D, Pal M, Konjengbam NS, Singh MP, Singh Sengar R, Sarker A. Comparative Inter- and IntraSpecies Transcriptomics Revealed Key Differential Pathways Associated With Aluminium Stress Tolerance in Lentil. FRONTIERS IN PLANT SCIENCE 2021; 12:693630. [PMID: 34531881 PMCID: PMC8438445 DOI: 10.3389/fpls.2021.693630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/30/2021] [Indexed: 05/28/2023]
Abstract
Aluminium stress causes plant growth retardation and engenders productivity loss under acidic soil conditions. This study accentuates morpho-physiological and molecular bases of aluminium (Al) tolerance within and between wild (ILWL-15) and cultivated (L-4602 and BM-4) lentil species. Morpho-physiological studies revealed better cyto-morphology of tolerant genotypes over sensitive under Al3+ stress conditions. Mitotic lesions were observed in root cells under these conditions. Transcriptome analysis under Al3+ stress revealed 30,158 specifically up-regulated genes in different comparison groups showing contigs between 15,305 and 18,861 bp. In tolerant genotypes, top up-regulated differentially expressed genes (DEGs) were found to be involved in organic acid synthesis and exudation, production of antioxidants, callose synthesis, protein degradation, and phytohormone- and calcium-mediated signalling under stress conditions. DEGs associated with epigenetic regulation and Al3+ sequestration inside vacuole were specifically upregulated in wild and cultivars, respectively. Based on assembled unigenes, an average of 6,645.7 simple sequence repeats (SSRs) and 14,953.7 high-quality single nucleotide polymorphisms (SNPs) were spotted. By quantitative real-time polymerase chain reaction (qRT-PCR), 12 selected genes were validated. Gene ontology (GO) annotation revealed a total of 8,757 GO terms in three categories, viz., molecular, biological, and cellular processes. Kyoto Encyclopaedia of Genes and Genomes pathway scanning also revealed another probable pathway pertaining to metacaspase-1,-4, and -9 for programmed cell death under Al-stress conditions. This investigation reveals key inter- and intraspecies metabolic pathways associated with Al-stress tolerance in lentil species that can be utilised in designing future breeding programmes to improve lentil and related species towards Al3+ stress.
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Affiliation(s)
- Chandan Kumar Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Dharmendra Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Jyoti Taunk
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Priya Chaudhary
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Shivani Chandra
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, India
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University—Imphal, Umiam, India
| | - M. Premjit Singh
- College of Agriculture, Central Agricultural University—Imphal, Iroisemba, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut, India
| | - Ashutosh Sarker
- International Center for Agriculture Research in the Dry Areas, New Delhi, India
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15
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Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM. Molecular topography of an entire nervous system. Cell 2021; 184:4329-4347.e23. [PMID: 34237253 DOI: 10.1016/j.cell.2021.06.023] [Citation(s) in RCA: 280] [Impact Index Per Article: 93.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/09/2021] [Accepted: 06/14/2021] [Indexed: 02/08/2023]
Abstract
We have produced gene expression profiles of all 302 neurons of the C. elegans nervous system that match the single-cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses distinct codes of ∼23 neuropeptide genes and ∼36 neuropeptide receptors, delineating a complex and expansive "wireless" signaling network. To demonstrate the utility of this comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression and (2) reveal adhesion proteins with potential roles in process placement and synaptic specificity. Our expression data are available at https://cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity, and function throughout the C. elegans nervous system.
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Affiliation(s)
- Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), DCEXS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Alexis Weinreb
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Alec Barrett
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Chuan Xu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Erdem Varol
- Department of Statistics, Columbia University, New York, NY, USA
| | - Panos Oikonomou
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Lori Glenwinkel
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Rebecca McWhirter
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Abigail Poff
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Manasa Basavaraju
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ibnul Rafi
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Steven J Cook
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Alexander Abrams
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Berta Vidal
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Cyril Cros
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Marc Hammarlund
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA.
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16
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Yuan C, Chen M, Cai X. Advances in poly(rC)-binding protein 2: Structure, molecular function, and roles in cancer. Biomed Pharmacother 2021; 139:111719. [PMID: 34233389 DOI: 10.1016/j.biopha.2021.111719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023] Open
Abstract
Poly(rC)-binding protein 2 (PCBP2) is an RNA-binding protein that is characterized by its ability to interact with poly(C) with high affinity in a sequence-specific manner. PCBP2 contains three K homology domains, which are consensus RNA-binding domains that play a role in recognizing and combining with RNA and DNA. The specific structure and localization of PCBP2 lay the foundation for its multiple roles in transcriptional, posttranscriptional, and translational processes, even in iron metabolism. Numerous studies have indicated that PCBP2 expression is increased in many cancer types. PCBP2 is considered as an oncogene that promotes tumorigenesis, development of cancer cells, and metastasis. Here, we summarized the current evidence regarding PCBP2 in the proliferation, migration, invasion of cancer cells, and drug resistance, aiming to clarify the molecular mechanisms of PCBP2 in cancer. Results from this review suggest that an in-depth study of PCBP2 in cancer may provide novel biomarkers for prognostic or therapeutic purposes.
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Affiliation(s)
- Chendong Yuan
- Department of Vascular Surgery, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, Zhejiang 311800, China.
| | - Mingxiang Chen
- Department of Cardiovascular surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, Yubei 401120, China.
| | - Xiaolu Cai
- Department of Oncological Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.
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17
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Robinson H, Ruelcke JE, Lewis A, Bond CS, Fox AH, Bharti V, Wani S, Cloonan N, Lai A, Margolin D, Li L, Salomon C, Richards RS, Farrell A, Gardiner RA, Parton RG, Cristino AS, Hill MM. Caveolin-1-driven membrane remodelling regulates hnRNPK-mediated exosomal microRNA sorting in cancer. Clin Transl Med 2021; 11:e381. [PMID: 33931969 PMCID: PMC8031663 DOI: 10.1002/ctm2.381] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Caveolae proteins play diverse roles in cancer development and progression. In prostate cancer, non-caveolar caveolin-1 (CAV1) promotes metastasis, while CAVIN1 attenuates CAV1-induced metastasis. Here, we unveil a novel mechanism linking CAV1 to selective loading of exosomes with metastasis-promoting microRNAs. RESULTS We identify hnRNPK as a CAV1-regulated microRNA binding protein. In the absence of CAVIN1, non-caveolar CAV1 drives localisation of hnRPNK to multi-vesicular bodies (MVBs), recruiting AsUGnA motif-containing miRNAs and causing their release within exosomes. This process is dependent on the lipid environment of membranes as shown by cholesterol depletion using methyl-β-cyclodextrin or by treatment with n-3 polyunsaturated fatty acids. Consistent with a role in bone metastasis, knockdown of hnRNPK in prostate cancer PC3 cells abolished the ability of PC3 extracellular vesicles (EV) to induce osteoclastogenesis, and biofluid EV hnRNPK is elevated in metastatic prostate and colorectal cancer. CONCLUSIONS Taken together, these results support a novel pan-cancer mechanism for CAV1-driven exosomal release of hnRNPK and associated miRNA in metastasis, which is modulated by the membrane lipid environment.
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Affiliation(s)
- Harley Robinson
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Jayde E. Ruelcke
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
| | - Amanda Lewis
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Charles S. Bond
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Archa H. Fox
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
- The Harry Perkins Institute of Medical ResearchQEII Medical CentreNedlandsWAAustralia
| | - Vandhana Bharti
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Shivangi Wani
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Nicole Cloonan
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Andrew Lai
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
| | - David Margolin
- Maternal‐Fetal Medicine, Department of Obstetrics and GynecologyOchsner Clinic FoundationNew OrleansUSA
| | - Li Li
- Maternal‐Fetal Medicine, Department of Obstetrics and GynecologyOchsner Clinic FoundationNew OrleansUSA
| | - Carlos Salomon
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
- Maternal‐Fetal Medicine, Department of Obstetrics and GynecologyOchsner Clinic FoundationNew OrleansUSA
- Department of Clinical Biochemistry and Immunology, Faculty of PharmacyUniversity of ConcepciónConcepciónChile
| | - Renée S. Richards
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Aine Farrell
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
| | - Robert A. Gardiner
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
| | - Robert G. Parton
- Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
- Centre for Microscopy and MicroanalysisThe University of QueenslandSt LuciaQueenslandAustralia
| | - Alexandre S. Cristino
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
- Griffith Institute for Drug DiscoveryGriffith UniversityBrisbaneQueenslandAustralia
| | - Michelle M. Hill
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
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18
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Wu Y, Zhao H, Zhang EE, Liu N. Identification of PCBP1 as a Novel Modulator of Mammalian Circadian Clock. Front Genet 2021; 12:656571. [PMID: 33841513 PMCID: PMC8034388 DOI: 10.3389/fgene.2021.656571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/05/2021] [Indexed: 11/13/2022] Open
Abstract
The circadian clock governs our daily cycle of behavior and physiology. Previous studies have identified a handful of core clock components and hundreds of circadian modifiers. Here, we report the discovery that poly(C)-binding protein 1 (PCBP1), displaying a circadian expression pattern, was a novel circadian clock regulator. We found that knocking down PCBP1 resulted in period shortening in human U2OS cells, and that manipulations of PCBP1 expression altered the activity of CLOCK/BMAL1 in an E-box-based reporter assay. Further mechanistic study demonstrated that this clock function of PCBP1 appears to work by enhancing the association of Cryptochrome 1 (CRY1) with the CLOCK/BMAL1 complex, thereby negatively regulating the latter’s activation. Co-immunoprecipitation of PCBP1 and core clock molecules confirmed the interactions between PCBP1 and CRY1, and a time-course qPCR assay revealed the rhythmic expression of PCBP1 in mouse hearts in vivo. Given that the RNA interference of mushroom-body expressed (mub), the poly(rC) binding protein (PCBP) homolog of Drosophila, in the clock neurons also led to a circadian phenotype in the locomotor assay, our study deemed PCBP1 a novel clock modifier whose circadian regulatory mechanism is conserved during evolution.
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Affiliation(s)
- Yaling Wu
- Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization Technology, Hubei Normal University, Huangshi, China.,Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, China.,National Demonstration Center for Experimental Biology Education, Hubei Normal University, Huangshi, China.,College of Life Sciences, Hubei Normal University, Huangshi, China.,National Institute of Biological Sciences, Beijing, China
| | - Haijiao Zhao
- National Institute of Biological Sciences, Beijing, China
| | | | - Na Liu
- Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization Technology, Hubei Normal University, Huangshi, China.,Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, China.,National Demonstration Center for Experimental Biology Education, Hubei Normal University, Huangshi, China.,College of Life Sciences, Hubei Normal University, Huangshi, China.,National Institute of Biological Sciences, Beijing, China
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19
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Tran JR, Paulson DI, Moresco JJ, Adam SA, Yates JR, Goldman RD, Zheng Y. An APEX2 proximity ligation method for mapping interactions with the nuclear lamina. J Cell Biol 2021; 220:e202002129. [PMID: 33306092 PMCID: PMC7737704 DOI: 10.1083/jcb.202002129] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 01/13/2023] Open
Abstract
The nuclear lamina (NL) is a meshwork found beneath the inner nuclear membrane. The study of the NL is hindered by the insolubility of the meshwork and has driven the development of proximity ligation methods to identify the NL-associated/proximal proteins, RNA, and DNA. To simplify and improve temporal labeling, we fused APEX2 to the NL protein lamin-B1 to map proteins, RNA, and DNA. The identified NL-interacting/proximal RNAs show a long 3' UTR bias, a finding consistent with an observed bias toward longer 3' UTRs in genes deregulated in lamin-null cells. A C-rich motif was identified in these 3' UTR. Our APEX2-based proteomics identifies a C-rich motif binding regulatory protein that exhibits altered localization in lamin-null cells. Finally, we use APEX2 to map lamina-associated domains (LADs) during the cell cycle and uncover short, H3K27me3-rich variable LADs. Thus, the APEX2-based tools presented here permit identification of proteomes, transcriptomes, and genome elements associated with or proximal to the NL.
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Affiliation(s)
- Joseph R. Tran
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
| | - Danielle I. Paulson
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
- Horace Mann School, The Bronx, NY
| | - James J. Moresco
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Stephen A. Adam
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - John R. Yates
- The Scripps Research Institution, Department of Molecular Medicine, La Jolla, CA
| | - Robert D. Goldman
- Northwestern University, Feinberg School of Medicine, Department of Cell and Developmental Biology, Chicago, IL
| | - Yixian Zheng
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD
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20
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Rieger MA, King DM, Crosby H, Liu Y, Cohen BA, Dougherty JD. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements. Cell Rep 2020; 33:108531. [PMID: 33357440 DOI: 10.1101/401604] [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: 10/09/2018] [Revised: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 05/24/2023] Open
Abstract
CELF6 is a CELF-RNA-binding protein, and thus part of a protein family with roles in human disease; however, its mRNA targets in the brain are largely unknown. Using cross-linking immunoprecipitation and sequencing (CLIP-seq), we define its CNS targets, which are enriched for 3' UTRs in synaptic protein-coding genes. Using a massively parallel reporter assay framework, we test the consequence of CELF6 expression on target sequences, with and without mutating putative binding motifs. Where CELF6 exerts an effect on sequences, it is largely to decrease RNA abundance, which is reversed by mutating UGU-rich motifs. This is also the case for CELF3-5, with a protein-dependent effect on magnitude. Finally, we demonstrate that targets are derepressed in CELF6-mutant mice, and at least two key CNS proteins, FOS and FGF13, show altered protein expression levels and localization. Our works find, in addition to previously identified roles in splicing, that CELF6 is associated with repression of its CNS targets via the 3' UTR in vivo.
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Affiliation(s)
- Michael A Rieger
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dana M King
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Haley Crosby
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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21
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Rieger MA, King DM, Crosby H, Liu Y, Cohen BA, Dougherty JD. CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3' UTR Elements. Cell Rep 2020; 33:108531. [PMID: 33357440 PMCID: PMC7780154 DOI: 10.1016/j.celrep.2020.108531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 02/08/2023] Open
Abstract
CELF6 is a CELF-RNA-binding protein, and thus part of a protein family with roles in human disease; however, its mRNA targets in the brain are largely unknown. Using cross-linking immunoprecipitation and sequencing (CLIP-seq), we define its CNS targets, which are enriched for 3′ UTRs in synaptic protein-coding genes. Using a massively parallel reporter assay framework, we test the consequence of CELF6 expression on target sequences, with and without mutating putative binding motifs. Where CELF6 exerts an effect on sequences, it is largely to decrease RNA abundance, which is reversed by mutating UGU-rich motifs. This is also the case for CELF3–5, with a protein-dependent effect on magnitude. Finally, we demonstrate that targets are derepressed in CELF6-mutant mice, and at least two key CNS proteins, FOS and FGF13, show altered protein expression levels and localization. Our works find, in addition to previously identified roles in splicing, that CELF6 is associated with repression of its CNS targets via the 3′ UTR in vivo. Rieger et al. assay the function of the RNA-binding protein CELF6 by defining its targets in the brain. They show that CELF6 largely binds 3′ UTRs of synaptic mRNAs. Using a massively parallel reporter assay, they further show that CELF6 and other CELFs are associated with lower mRNA abundance and that targets are derepressed in Celf6-knockout mice in vivo.
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Affiliation(s)
- Michael A Rieger
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dana M King
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Haley Crosby
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA.
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22
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Zheng KW, Zhang JY, He YD, Gong JY, Wen CJ, Chen JN, Hao YH, Zhao Y, Tan Z. Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic Acids Res 2020; 48:11706-11720. [PMID: 33045726 PMCID: PMC7672459 DOI: 10.1093/nar/gkaa841] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 01/08/2023] Open
Abstract
G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123 000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ∼70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.
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Affiliation(s)
- Ke-wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Jia-yu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multidisciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yi-de He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Jia-yuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Cui-jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Juan-nan Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Yu-hua Hao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Yong Zhao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- Center for Healthy Aging, Changzhi Medical College, Changzhi 046000, Shanxi, P.R. China
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Ishii T, Igawa T, Hayakawa H, Fujita T, Sekiguchi M, Nakabeppu Y. PCBP1 and PCBP2 both bind heavily oxidized RNA but cause opposing outcomes, suppressing or increasing apoptosis under oxidative conditions. J Biol Chem 2020; 295:12247-12261. [PMID: 32647012 PMCID: PMC7443489 DOI: 10.1074/jbc.ra119.011870] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 07/06/2020] [Indexed: 12/18/2022] Open
Abstract
PCBP1, a member of the poly(C)-binding protein (PCBP) family, has the capability of binding heavily oxidized RNA and therefore participates in the cellular response to oxidative conditions, helping to induce apoptosis. There are four other members of this family, PCBP2, PCBP3, PCBP4, and hnRNPK, but it is not known whether they play similar roles. To learn more, we first tested their affinity for an RNA strand carrying two 8-oxoguanine (8-oxoG) residues at sites located in close proximity to each other, representative of a heavily oxidized strand or RNA with one 8-oxoG or none. Among them, only PCBP2 exhibited highly selective binding to RNA carrying two 8-oxoG residues similar to that observed with PCBP1. In contrast, PCBP3, PCBP4, and hnRNPK bound RNA with or without 8-oxoG modifications and exhibited slightly increased binding to the former. Mutations in conserved RNA-binding domains of PCBP2 disrupted the specific interaction with heavily oxidized RNA. We next tested PCBP2 activity in cells. Compared with WT HeLa S3 cells, PCBP2-KO cells established by gene editing exhibited increased apoptosis with increased caspase-3 activity and PARP1 cleavage under oxidative conditions, which were suppressed by the expression of WT PCBP2 but not one of the mutants lacking binding activity. In contrast, PCBP1-KO cells exhibited reduced apoptosis with much less caspase-3 activity and PARP cleavage than WT cells. Our results indicate that PCBP2 as well as PCBP1 bind heavily oxidized RNA; however, the former may counteract PCBP1 to suppress apoptosis under oxidative conditions.
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Affiliation(s)
- Takashi Ishii
- Department of Biochemistry, Fukuoka Dental College, Fukuoka, Japan; Oral Medicine Research Center, Fukuoka Dental College, Fukuoka, Japan
| | - Tatsuhiro Igawa
- Frontier Research Center, Fukuoka Dental College, Fukuoka, Japan
| | - Hiroshi Hayakawa
- Department of Biochemistry, Fukuoka Dental College, Fukuoka, Japan
| | - Tsugumi Fujita
- Department of Biochemistry, Fukuoka Dental College, Fukuoka, Japan
| | - Mutsuo Sekiguchi
- Frontier Research Center, Fukuoka Dental College, Fukuoka, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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Bogolyubova I, Bogolyubov D. Heterochromatin Morphodynamics in Late Oogenesis and Early Embryogenesis of Mammals. Cells 2020; 9:cells9061497. [PMID: 32575486 PMCID: PMC7348780 DOI: 10.3390/cells9061497] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
During the period of oocyte growth, chromatin undergoes global rearrangements at both morphological and molecular levels. An intriguing feature of oogenesis in some mammalian species is the formation of a heterochromatin ring-shaped structure, called the karyosphere or surrounded "nucleolus", which is associated with the periphery of the nucleolus-like bodies (NLBs). Morphologically similar heterochromatin structures also form around the nucleolus-precursor bodies (NPBs) in zygotes and persist for several first cleavage divisions in blastomeres. Despite recent progress in our understanding the regulation of gene silencing/expression during early mammalian development, as well as the molecular mechanisms that underlie chromatin condensation and heterochromatin structure, the biological significance of the karyosphere and its counterparts in early embryos is still elusive. We pay attention to both the changes of heterochromatin morphology and to the molecular mechanisms that can affect the configuration and functional activity of chromatin. We briefly discuss how DNA methylation, post-translational histone modifications, alternative histone variants, and some chromatin-associated non-histone proteins may be involved in the formation of peculiar heterochromatin structures intimately associated with NLBs and NPBs, the unique nuclear bodies of oocytes and early embryos.
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25
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Ouyang S, Jia B, Xie W, Yang J, Lv Y. Mechanism underlying the regulation of sortilin expression and its trafficking function. J Cell Physiol 2020; 235:8958-8971. [PMID: 32474917 DOI: 10.1002/jcp.29818] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022]
Abstract
This review summarizes and analyzes the updated information on the regulation of sortilin expression and its trafficking function. Evidence indicates that the expression and function of sortilin are closely regulated at four levels: DNA, messenger RNA (mRNA), protein, and trafficking function. DNA methylation, several mutations, and minor single-nucleotide polymorphisms within DNA fragments affect the expression of SORT1 gene. A few transcription factors and microRNAs modulate its transcription as well as the splicing or stability of the mRNA. Moreover, several translation factors control the synthesis of sortilin protein, and posttranslational modifications affect its degradation processes. Multiple adaptor molecules modulate the sortilin trafficking function in the anterograde or retrograde pathway. Recent advances in the regulation of sortilin expression and function, and its related mechanisms will help the ongoing research related to sortilin and promote future clinical application via sortilin intervention.
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Affiliation(s)
- Shuhui Ouyang
- Department of Anatomy, Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical College, University of South China, Hengyang, China
| | - Bo Jia
- Department of Anatomy, Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical College, University of South China, Hengyang, China
| | - Wei Xie
- Department of Anatomy, Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical College, University of South China, Hengyang, China
| | - Jing Yang
- Department of Endocrinology of the First Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Yuncheng Lv
- Department of Anatomy, Clinical Anatomy & Reproductive Medicine Application Institute, Hengyang Medical College, University of South China, Hengyang, China.,Guangxi Key Laboratory of Diabetic Systems Medicine, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin, China
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26
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Gong B, Wang X, Li B, Li Y, Lu R, Zhang K, Li B, Ma Y, Li Y. miR-205-5p inhibits thymic epithelial cell proliferation via FA2H-TFAP2A feedback regulation in age-associated thymus involution. Mol Immunol 2020; 122:173-185. [PMID: 32371259 DOI: 10.1016/j.molimm.2020.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/02/2020] [Accepted: 04/13/2020] [Indexed: 12/28/2022]
Abstract
Thymic epithelial cells (TECs) are essential regulators of T cell development and selection. microRNAs (miRNAs) play critical roles in regulating TECs proliferation during thymus involution. miR-205-5p is highly expressed in TECs and increases with age. However, the function and potential mechanism of miR-205-5p in TECs are not clear. miRNA expression was profiled using TECs from male and female mice at 1 and 3 months old. A total of 325 differentially expressed miRNAs (DEMs) were detected at different ages in two sexes. 24 of the DEMs had the same trend between males and females. Among them, miR-205-5p had the highest fold change. Our results showed that the expression of miR-205-5p was dramatically increased in TECs from 1 to 9 months old mice. miR-205-5p mimic inhibited TECs proliferation. Moreover, we confirmed that Fa2h was the direct target gene of miR-205-5p and FA2H was significantly decreased in TECs with increased expression of miR-205-5p. Silencing of Fa2h inhibited TECs proliferation. Furthermore, we found that the expression of Tfap2a could be promoted by FA2H and that TFAP2A could interact with miR-205-5p in TECs. Overall, miR-205-5p is an important regulator of TECs proliferation and regulates age-associated thymus involution via the miR-205-5p-FA2H-TFAP2A feedback regulatory circuit. miR-205-5p might act as a potential biomarker in TECs for age-related thymus involution.
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Affiliation(s)
- Bishuang Gong
- College of Veterinary Medicine, South China Agricultural University, China
| | - Xintong Wang
- College of Veterinary Medicine, South China Agricultural University, China
| | - Boning Li
- the Department of Cardiology, Shenzhen Children's Hospital, Shenzhen, China
| | - Ying Li
- College of Veterinary Medicine, South China Agricultural University, China
| | - Rui Lu
- College of Veterinary Medicine, South China Agricultural University, China
| | - Kaizhao Zhang
- College of Veterinary Medicine, South China Agricultural University, China
| | - Bingxin Li
- College of Veterinary Medicine, South China Agricultural University, China
| | - Yongjiang Ma
- College of Veterinary Medicine, South China Agricultural University, China.
| | - Yugu Li
- College of Veterinary Medicine, South China Agricultural University, China.
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27
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Xu Y, Wu W, Han Q, Wang Y, Li C, Zhang P, Xu H. Post-translational modification control of RNA-binding protein hnRNPK function. Open Biol 2020; 9:180239. [PMID: 30836866 PMCID: PMC6451366 DOI: 10.1098/rsob.180239] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNPK), a ubiquitously occurring RNA-binding protein (RBP), can interact with numerous nucleic acids and various proteins and is involved in a number of cellular functions including transcription, translation, splicing, chromatin remodelling, etc. Through its abundant biological functions, hnRNPK has been implicated in cellular events including proliferation, differentiation, apoptosis, DNA damage repair and the stress and immune responses. Thus, it is critical to understand the mechanism of hnRNPK regulation and its downstream effects on cancer and other diseases. A number of recent studies have highlighted that several post-translational modifications (PTMs) possibly play an important role in modulating hnRNPK function. Phosphorylation is the most widely occurring PTM in hnRNPK. For example, in vivo analyses of sites such as S116 and S284 illustrate the purpose of PTM of hnRNPK in altering its subcellular localization and its ability to bind target nucleic acids or proteins. Other PTMs such as methylation, ubiquitination, sumoylation, glycosylation and proteolytic cleavage are increasingly implicated in the regulation of DNA repair, cellular stresses and tumour growth. In this review, we describe the PTMs that impact upon hnRNPK function on gene expression programmes and different disease states. This knowledge is key in allowing us to better understand the mechanism of hnRNPK regulation.
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Affiliation(s)
- Yongjie Xu
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Wei Wu
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Qiu Han
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Yaling Wang
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Cencen Li
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Pengpeng Zhang
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Haixia Xu
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
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28
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hnRNP K Supports High-Amplitude D Site-Binding Protein mRNA ( Dbp mRNA) Oscillation To Sustain Circadian Rhythms. Mol Cell Biol 2020; 40:MCB.00537-19. [PMID: 31907279 DOI: 10.1128/mcb.00537-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/20/2019] [Indexed: 01/24/2023] Open
Abstract
Circadian gene expression is defined by the gene-specific phase and amplitude of daily oscillations in mRNA and protein levels. D site-binding protein mRNA (Dbp mRNA) shows high-amplitude oscillation; however, the underlying mechanism remains elusive. Here, we demonstrate that heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a key regulator that activates Dbp transcription via the poly(C) motif within its proximal promoter. Biochemical analyses identified hnRNP K as a specific protein that directly associates with the poly(C) motif in vitro Interestingly, we further confirmed the rhythmic binding of endogenous hnRNP K within the Dbp promoter through chromatin immunoprecipitation as well as the cycling expression of hnRNP K. Finally, knockdown of hnRNP K decreased mRNA oscillation in both Dbp and Dbp-dependent clock genes. Taken together, our results show rhythmic protein expression of hnRNP K and provide new insights into its function as a transcriptional amplifier of Dbp.
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29
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Dukovski D, Villella A, Bastos C, King R, Finley D, Kelly JW, Morimoto RI, Hartl FU, Munoz B, Lee PS, Zecevic M, Miller JP. Amplifiers co-translationally enhance CFTR biosynthesis via PCBP1-mediated regulation of CFTR mRNA. J Cyst Fibros 2020; 19:733-741. [PMID: 32067958 DOI: 10.1016/j.jcf.2020.02.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/01/2020] [Accepted: 02/06/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Cystic fibrosis (CF) is a recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We previously described a first-in-class CFTR modulator that functions as an amplifier to selectively increase CFTR expression and function. The amplifier mechanism is distinct from and complementary to corrector and potentiator classes of CFTR modulators. Here we characterize the mechanism by which amplifiers increase CFTR mRNA, protein, and activity. METHODS Biochemical studies elucidated the action of amplifiers on CFTR mRNA abundance and translation and defined the role of an amplifier-binding protein that was identified using chemical proteomics. RESULTS Amplifiers stabilize CFTR mRNA through a process that requires only the translated sequence of CFTR and involves translational elongation. Amplifiers enrich ER-associated CFTR mRNA and increase its translational efficiency through increasing the fraction of CFTR mRNA associated with polysomes. Pulldowns identified the poly(rC)-binding protein 1 (PCBP1) as directly binding to amplifier. A PCBP1 consensus element was identified within the CFTR open reading frame that binds PCBP1. This sequence proved necessary for amplifier responsiveness. CONCLUSIONS Small molecule amplifiers co-translationally increase CFTR mRNA stability. They enhance translation through addressing the inherently inefficient membrane targeting of CFTR mRNA. Amplifiers bind directly to PCBP1, show enhanced affinity in the presence of bound RNA, and require a PCBP1 consensus element within CFTR mRNA to elicit translational effects. These modulators represent a promising new and mechanistically novel class of CFTR therapeutic. They may be useful as a monotherapy or in combination with other CFTR modulators.
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Affiliation(s)
- Danijela Dukovski
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Adriana Villella
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Cecilia Bastos
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Randall King
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Jeffery W Kelly
- Departments of Molecular Medicine and Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Richard I Morimoto
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, United States
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Benito Munoz
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Po-Shun Lee
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - Marija Zecevic
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States
| | - John Preston Miller
- Proteostasis Therapeutics, Inc., 80 Guest St, Suite 500, Boston, MA 02135, United States.
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30
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Functional expression of ZNF467 and PCBP2 supports adipogenic lineage commitment in adipose-derived mesenchymal stem cells. Gene 2020; 737:144437. [PMID: 32032745 DOI: 10.1016/j.gene.2020.144437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 01/13/2023]
Abstract
Bone marrow-derived mesenchymal stromal/stem cells (BMSCs) have the potential to be employed in many different skeletal therapies. A major limitation to utilizing BMSCs as a therapeutic strategy in human disease and tissue regeneration is the low cell numbers obtained from initial isolation necessitating multiple cell passages that can lead to decreased cell quality. Adipose-derived mesenchymal stromal/stem cells (AMSCs) have been proposed as an alternative cell source for regenerative therapies; however the differentiation capacity of these cells differs from BMSCs. To understand the differences between BMSCs and AMSCs, we compared the global gene expression profiles of BMSCs and AMSCs and identified two genes, PCBP2 and ZNF467 that were differentially expressed between AMSCs and BMSCs. We demonstrate that PCBP2 and ZNF467 impact adipogenic but not osteogenic differentiation, further supporting evidence that AMSCs and BMSCs appear to be adapted to their microenvironment.
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31
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Expression patterns of pcbp gene family members during zebrafish embryogenesis. Gene Expr Patterns 2020; 35:119097. [PMID: 32007595 DOI: 10.1016/j.gep.2020.119097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/14/2020] [Accepted: 01/27/2020] [Indexed: 10/25/2022]
Abstract
The poly(C)-binding protein (PCBP) family members belong to a subtype of RNA-binding proteins that are ubiquitously expressed with diverse functions. In mammals, PCBP family, also known as hnRNP E family, is composed of four proteins, namely PCBP1, PCBP2, PCBP3 and PCBP4. So far, no study has been documented on the physiological roles of each member in vertebrate development. Here we analysed the spatiotemporal expression patterns of zebrafish (Danio rerio) pcbp2 (identical to pcbp1 and pcbp2 in mammals), pcbp3 and pcbp4 at various stages of zebrafish embryonic development by whole-mount in situ hybridization. Our results revealed that all pcbp genes are maternally expressed, especially pcbp2, which is strongly expressed from the embryogenetic stage to larva. The expression patterns of PCBP members are similar to each other at the very early developmental stage sharing with common strong expression in the intestine, otic vesicle, retina and brain of zebrafish. Subsequently, the messenger RNAs of PCBP members are gradually constrained and highly expressed in intestines of the larvae. Collectively, our study figured out the expression pattern of each PCBP member in diverse organogenesis during embryo development, indicating that PCBP members may play predominant roles in the development of neural and digestive systems to maintain their normal physiological functions. Moreover, the similar expression patterns at the developmental stages and organ types among this family suggest that the aberrant expression of these genes would lead to the neural or intestinal diseases.
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32
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Jiang H, Hou P, He H, Wang H. Cell apoptosis regulated by interaction between viral gene alpha 3 and host heterogeneous nuclear ribonucleoprotein K facilitates bovine ephemeral fever virus replication. Vet Microbiol 2020; 240:108510. [DOI: 10.1016/j.vetmic.2019.108510] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 02/06/2023]
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33
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Garland W, Jensen TH. Nuclear sorting of RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1572. [PMID: 31713323 DOI: 10.1002/wrna.1572] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/27/2022]
Abstract
The majority of the mammalian genome is transcribed by RNA polymerase II, yielding a vast amount of noncoding RNA (ncRNA) in addition to the standard production of mRNA. The typical nuclear biogenesis of mRNA relies on the tightly controlled coupling of co- and post-transcriptional processing events, which ultimately results in the export of transcripts into the cytoplasm. These processes are subject to surveillance by nuclear RNA decay pathways to prevent the export of aberrant, or otherwise "non-optimal," transcripts. However, unlike mRNA, many long ncRNAs are nuclear retained and those that maintain enduring functions must employ precautions to evade decay. Proper sorting and localization of RNA is therefore an essential activity in eukaryotic cells and the formation of ribonucleoprotein complexes during early stages of RNA synthesis is central to deciding such transcript fate. This review details our current understanding of the pathways and factors that direct RNAs towards a particular destiny and how transcripts combat the adverse conditions of the nucleus. This article is categorized under: RNA Export and Localization > Nuclear Export/Import RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C., Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C., Denmark
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34
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Kajino T, Shimamura T, Gong S, Yanagisawa K, Ida L, Nakatochi M, Griesing S, Shimada Y, Kano K, Suzuki M, Miyano S, Takahashi T. Divergent lncRNA MYMLR regulates MYC by eliciting DNA looping and promoter-enhancer interaction. EMBO J 2019; 38:e98441. [PMID: 31361039 DOI: 10.15252/embj.201798441] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 06/13/2019] [Accepted: 06/21/2019] [Indexed: 12/30/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) function in a wide range of processes by diverse mechanisms, though their roles in regulation of oncogenes and/or tumor suppressors remain rather elusive. We performed a global search for lncRNAs affecting MYC activity using a systems biology-based approach with a K supercomputer and the GIMLET algorism based on local distance correlations. Consequently, MYMLR was identified and experimentally shown to maintain MYC transcriptional activity and cell cycle progression despite the low levels of expression. A proteomic search for MYMLR-binding proteins identified PCBP2, while it was also found that MYMLR places a 557-kb upstream enhancer region in the proximity of the MYC promoter in cooperation with PCBP2. These findings implicate a crucial role for MYMLR in regulation of the archetypical oncogene MYC and warrant future studies regarding the involvement of low copy number lncRNAs in regulation of other crucial oncogenes and tumor suppressor genes.
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Affiliation(s)
- Taisuke Kajino
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shuyi Gong
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kiyoshi Yanagisawa
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Lisa Ida
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Nakatochi
- Statistical Analysis Section, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Sebastian Griesing
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukako Shimada
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Keiko Kano
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoshi Suzuki
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takashi Takahashi
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Aichi Cancer Center, Nagoya, Japan
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The Poly(C) Motif in the Proximal Promoter Region of the D Site-Binding Protein Gene ( Dbp) Drives Its High-Amplitude Oscillation. Mol Cell Biol 2019; 39:MCB.00101-19. [PMID: 31160492 DOI: 10.1128/mcb.00101-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/28/2019] [Indexed: 11/20/2022] Open
Abstract
The D site-binding protein (Dbp) supports the rhythmic transcription of downstream genes, in part by displaying high-amplitude cycling of its own transcripts compared to other circadian-clock genes. However, the underlying mechanism remains elusive. Here, we demonstrated that the poly(C) motif within the Dbp proximal promoter, in addition to an E-box element, provoked transcriptional activation. Furthermore, we generated a cell line with poly(C) deleted to demonstrate the endogenous effect of the poly(C) motif within the Dbp promoter. We investigated whether RNA polymerase 2 (Pol2) recruitment on the Dbp promoter was decreased in the cell line with poly(C) deleted. Next, assay for transposase-accessible chromatin (ATAC)-quantitative PCR (qPCR) showed that the poly(C) motif induced greater chromatin accessibility within the region of the Dbp promoter. Finally, we determined that the oscillation amplitude of endogenous Dbp mRNA of the cell line with poly(C) deleted was decreased, which affected the oscillation of other clock genes that are controlled by Dbp Taken together, our results provide new insights into the function of the poly(C) motif as a novel cis-acting element of Dbp, along with its significance in the regulation of circadian rhythms.
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Nazarov IB, Bakhmet EI, Tomilin AN. KH-Domain Poly(C)-Binding Proteins as Versatile Regulators of Multiple Biological Processes. BIOCHEMISTRY (MOSCOW) 2019; 84:205-219. [PMID: 31221059 DOI: 10.1134/s0006297919030039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Five known members of the family of KH-domain poly(C)-binding proteins (Pcbp1-4, hnRNP-K) have an unusually broad spectrum of cellular functions that include regulation of gene transcription, regulation of pre-mRNA processing, splicing, mRNA stability, translational silencing and enhancement, the control of iron turnover, and many others. Mechanistically, these proteins act via nucleic acid binding and protein-protein interactions. Through performing these multiple tasks, the KH-domain poly(C)-binding family members are involved in a wide variety of biological processes such as embryonic development, cell differentiation, and cancer. Deregulation of KH-domain protein expression is frequently associated with severe developmental defects and neoplasia. This review summarizes progress in studies of the KH-domain proteins made over past two decades. The review also reports our recent finding implying an involvement of the KH-factor Pcbp1 into control of transition from naïve to primed pluripotency cell state.
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Affiliation(s)
- I B Nazarov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
| | - E I Bakhmet
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
| | - A N Tomilin
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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38
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Ishii T, Sekiguchi M. Two ways of escaping from oxidative RNA damage: Selective degradation and cell death. DNA Repair (Amst) 2019; 81:102666. [PMID: 31326364 DOI: 10.1016/j.dnarep.2019.102666] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Reactive oxygen species (ROS) are produced during normal cellular metabolism, and various oxidized compounds are formed by the ROS attack. Among oxidized bases, 8-oxo-7,8-dihydroguanine (8-oxoG) is most abundant and seems important with respect to the maintenance and transfer of genetic information. The accumulation of 8-oxoG in messenger RNA may cause errors during codon-anticodon pairing in the translation process, which may result in the synthesis of abnormal proteins. Organisms that use oxygen as the source of energy production must therefore have some mechanisms to eliminate the deleterious effects of RNA oxidation. Recently, we found two protein factors, AUF1 and PCBP1, which each have a different binding capacity to oxidized RNA. Evidence demonstrated that AUF1 is involved in the specific degradation of oxidized RNA, and that PCBP1 has a function of inducing cell death to eliminate severely damaged RNA.
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Affiliation(s)
- Takashi Ishii
- Department of Biochemistry, Fukuoka Dental College, Fukuoka 814-0193, Japan.
| | - Mutsuo Sekiguchi
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
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Smirnova VV, Shestakova ED, Bikmetov DV, Chugunova AA, Osterman IA, Serebryakova MV, Sergeeva OV, Zatsepin TS, Shatsky IN, Terenin IM. eIF4G2 balances its own mRNA translation via a PCBP2-based feedback loop. RNA (NEW YORK, N.Y.) 2019; 25:757-767. [PMID: 31010886 PMCID: PMC6573783 DOI: 10.1261/rna.065623.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Poly(rC)-binding protein 2 (PCBP2, hnRNP E2) is one of the most abundant RNA-binding proteins in mammalian cells. In humans, it exists in seven isoforms, which are assumed to play similar roles in cells. The protein is shown to bind 3'-untranslated regions (3'-UTRs) of many mRNAs and regulate their translation and/or stability, but nothing is known about the functional consequences of PCBP2 binding to 5'-UTRs. Here we show that the PCBP2 isoform f interacts with the 5'-UTRs of mRNAs encoding eIF4G2 (a translation initiation factor with a yet unknown mechanism of action, also known as DAP5) and Cyclin I, and inhibits their translation in vitro and in cultured cells, while the PCBP2 isoform e only affects Cyclin I translation. Furthermore, eIF4G2 participates in a cap-dependent translation of the PCBP2 mRNA. Thus, PCBP2 and eIF4G2 seem to regulate one another's expression via a novel type of feedback loop formed by the translation initiation factor and the RNA-binding protein.
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Affiliation(s)
- Victoria V Smirnova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - Ekaterina D Shestakova
- Department of Biochemistry, School of Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, 119234, Russian Federation
| | - Dmitry V Bikmetov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
| | - Anastasia A Chugunova
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Ilya A Osterman
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - Olga V Sergeeva
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Timofey S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russian Federation
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40
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Bakhmet EI, Nazarov IB, Gazizova AR, Vorobyeva NE, Kuzmin AA, Gordeev MN, Sinenko SA, Aksenov ND, Artamonova TO, Khodorkovskii MA, Alenina N, Onichtchouk D, Wu G, Schöler HR, Tomilin AN. hnRNP-K Targets Open Chromatin in Mouse Embryonic Stem Cells in Concert with Multiple Regulators. Stem Cells 2019; 37:1018-1029. [PMID: 31021473 DOI: 10.1002/stem.3025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 01/02/2023]
Abstract
The transcription factor Oct4 plays a key regulatory role in the induction and maintenance of cellular pluripotency. In this article, we show that ubiquitous and multifunctional poly(C) DNA/RNA-binding protein hnRNP-K occupies Oct4 (Pou5f1) enhancers in embryonic stem cells (ESCs) but is dispensable for the initiation, maintenance, and downregulation of Oct4 gene expression. Nevertheless, hnRNP-K has an essential cell-autonomous function in ESCs to maintain their proliferation and viability. To better understand mechanisms of hnRNP-K action in ESCs, we have performed ChIP-seq analysis of genome-wide binding of hnRNP-K and identified several thousands of hnRNP-K target sites that are frequently co-occupied by pluripotency-related and common factors (Oct4, TATA-box binding protein, Sox2, Nanog, Otx2, etc.), as well as active histone marks. Furthermore, hnRNP-K localizes exclusively within open chromatin, implying its role in the onset and/or maintenance of this chromatin state. Stem Cells 2019;37:1018-1029.
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Affiliation(s)
- Evgeny I Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Igor B Nazarov
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Adel R Gazizova
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Nadezhda E Vorobyeva
- Group of transcriptional complexes dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey A Kuzmin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Mikhail N Gordeev
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Sergey A Sinenko
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Nikolai D Aksenov
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Tatyana O Artamonova
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Mikhail A Khodorkovskii
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Natalia Alenina
- Molecular Biology of Peptide Hormones, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Daria Onichtchouk
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max-Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max-Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Alexey N Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.,Laboratory of Cellular and Molecular Biology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
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Molineros JE, Singh B, Terao C, Okada Y, Kaplan J, McDaniel B, Akizuki S, Sun C, Webb CF, Looger LL, Nath SK. Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility. Front Immunol 2019; 10:1066. [PMID: 31164884 PMCID: PMC6536009 DOI: 10.3389/fimmu.2019.01066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/25/2019] [Indexed: 11/21/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component. We recently identified a novel SLE susceptibility locus near RASGRP1, which governs the ERK/MAPK kinase cascade and B-/T-cell differentiation and development. However, precise causal RASGRP1 functional variant(s) and their mechanisms of action in SLE pathogenesis remain undefined. Our goal was to fine-map this locus, prioritize genetic variants likely to be functional, experimentally validate their biochemical mechanisms, and determine the contribution of these SNPs to SLE risk. We performed a meta-analysis across six Asian and European cohorts (9,529 cases; 22,462 controls), followed by in silico bioinformatic and epigenetic analyses to prioritize potentially functional SNPs. We experimentally validated the functional significance and mechanism of action of three SNPs in cultured T-cells. Meta-analysis identified 18 genome-wide significant (p < 5 × 10−8) SNPs, mostly concentrated in two haplotype blocks, one intronic and the other intergenic. Epigenetic fine-mapping, allelic, eQTL, and imbalance analyses predicted three transcriptional regulatory regions with four SNPs (rs7170151, rs11631591-rs7173565, and rs9920715) prioritized for functional validation. Luciferase reporter assays indicated significant allele-specific enhancer activity for intronic rs7170151 and rs11631591-rs7173565 in T-lymphoid (Jurkat) cells, but not in HEK293 cells. Following up with EMSA, mass spectrometry, and ChIP-qPCR, we detected allele-dependent interactions between heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and rs11631591. Furthermore, inhibition of hnRNP-K in Jurkat and primary T-cells downregulated RASGRP1 and ERK/MAPK signaling. Comprehensive association, bioinformatics, and epigenetic analyses yielded putative functional variants of RASGRP1, which were experimentally validated. Notably, intronic variant (rs11631591) is located in a cell type-specific enhancer sequence, where its risk allele binds to the hnRNP-K protein and modulates RASGRP1 expression in Jurkat and primary T-cells. As risk allele dosage of rs11631591 correlates with increased RASGRP1 expression and ERK activity, we suggest that this SNP may underlie SLE risk at this locus.
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Affiliation(s)
- Julio E Molineros
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Bhupinder Singh
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Chikashi Terao
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jakub Kaplan
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Barbara McDaniel
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Shuji Akizuki
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Carol F Webb
- Departments of Medicine, Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Loren L Looger
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, United States
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
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Abstract
Many past and recent advances in the field of iron metabolism have relied upon the discovery of divalent metal transporter 1, DMT1 in 1997. DMT1 is the major iron transporter and contributes non-heme iron uptake in most types of cell. Each DMT1 isoform exhibits different expression patterns in cell-type specificity and distinct subcellular distribution, which enables cells to uptake both transferrin-bound and non-transferrin-bound irons efficiently. DMT1 expression is regulated by iron through the translational and degradation pathways to ensure iron homeostasis. It is considered that mammalian iron transporters including DMT1 cannot transport ferric iron but ferrous iron. Being reduced to ferrous state is likely to damage cells and tissues through the production of reactive oxygen species. Recently, iron chaperones have been identified, which can provide an answer to how ferrous iron is transported safely in cytosol. We summarize DMT1 expression depending on the types of cell or tissue and the function and mechanism of one of the iron chaperones, PCBP2.
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Affiliation(s)
- Izumi Yanatori
- Department of Biochemistry, Stanford University, School of Medicine, 279 Campus Drive, Stanford, CA 94305-5307, USA
| | - Fumio Kishi
- Hagi Public Health and Welfare Center, Yamaguchi Prefectural Government, 531-1 Emukai, Hagi, Yamaguchi 758-0041, Japan.
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Characterization of acute myeloid leukemia with del(9q) - Impact of the genes in the minimally deleted region. Leuk Res 2018; 76:15-23. [PMID: 30476680 DOI: 10.1016/j.leukres.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/13/2018] [Accepted: 11/15/2018] [Indexed: 02/06/2023]
Abstract
Acute myeloid leukemia is an aggressive disease that arises from clonal expansion of malignant hematopoietic precursor cells of the bone marrow. Deletions on the long arm of chromosome 9 (del(9q)) are observed in 2% of acute myeloid leukemia patients. Our deletion analysis in a cohort of 31 del(9q) acute myeloid leukemia patients further supports the importance of a minimally deleted region composed of seven genes potentially involved in leukemogenesis: GKAP1, KIF27, C9ORF64, HNRNPK, RMI1, SLC28A3 and NTRK2. Importantly, among them HNRNPK, encoding heterogeneous nuclear ribonucleoprotein K is proposed to function in leukemogenesis. We show that expression of HNRNPK and the other genes of the minimally deleted region is significantly reduced in patients with del(9q) compared with normal karyotype acute myeloid leukemia. Also, two mRNAs interacting with heterogeneous nuclear ribonucleoprotein K, namely CDKN1A and CEBPA are significantly downregulated. While the deletion size is not correlated with outcome, associated genetic aberrations are important. Patients with an additional t(8;21) show a good prognosis. RUNX1-RUNX1T1, which emerges from the t(8;21) leads to transcriptional down-regulation of CEBPA. Acute myeloid leukemia patients with mutations in CEBPA have a good prognosis as well. Interestingly, in del(9q) patients with CEBPA mutation mRNA levels of HNRNPK and the other genes located in the minimally deleted region is restored to normal karyotype level. Our data indicate that a link between CEBPA and the genes of the minimally deleted region, among them HNRNPK contributes to leukemogenesis in acute myeloid leukemia with del(9q).
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Shi H, Li H, Yuan R, Guan W, Zhang X, Zhang S, Zhang W, Tong F, Li L, Song Z, Wang C, Yang S, Wang H. PCBP1 depletion promotes tumorigenesis through attenuation of p27 Kip1 mRNA stability and translation. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:187. [PMID: 30086790 PMCID: PMC6081911 DOI: 10.1186/s13046-018-0840-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/10/2018] [Indexed: 11/10/2022]
Abstract
Background Poly C Binding Protein 1 (PCBP1) is an RNA-binding protein that binds and regulates translational activity of subsets of cellular mRNAs. Depletion of PCBP1 is implicated in various carcinomas, but the underlying mechanism in tumorigenesis remains elusive. Methods We performed a transcriptome-wide screen to identify novel bounding mRNA of PCBP1. The bind regions between PCBP1 with target mRNA were investigated by using point mutation and luciferase assay. Cell proliferation, cell cycle, tumorigenesis and cell apoptosis were also evaluated in ovary and colon cancer cell lines. The mechanism that PCBP1 affects p27 was analyzed by mRNA stability and ribosome profiling assays. We analyzed PCBP1 and p27 expression in ovary, colon and renal tumor samples and adjacent non-tumor tissues using RT-PCR, Western Blotting and immunohistochemistry. The prognostic significance of PCBP1 and p27 also analyzed using online databases. Results We identified cell cycle inhibitor p27Kip1 (p27) as a novel PCBP1-bound transcript. We then demonstrated that binding of PCBP1 to p27 3’UTR via its KH1 domain mainly stabilizes p27 mRNA, while enhances its translation to fuel p27 expression, prior to p27 protein degradation. The upregulated p27 consequently inhibits cell proliferation, cell cycle progression and tumorigenesis, whereas promotes cell apoptosis under paclitaxel treatment. Conversely, knockdown of PCBP1 in turn compromises p27 mRNA stability, leading to lower p27 level and tumorigenesis in vivo. Moreover, forced depletion of p27 counteracts the tumor suppressive ability of PCBP1 in the same PCBP1 over-expressing cells. Physiologically, we showed that decreases of both p27 mRNA and its protein expressions are well correlated to PCBP1 depletion in ovary, colon and renal tumor samples, independent of the p27 ubiquitin ligase Skp2 level. Correlation of PCBP1 with p27 is also found in the tamoxifen, doxorubincin and lapatinib resistant breast cancer cells of GEO database. Conclusion Our results thereby indicate that loss of PCBP1 expression firstly attenuates p27 expression at post-transcriptional level, and subsequently promotes carcinogenesis. PCBP1 could be used as a diagnostic marker to cancer patients. Electronic supplementary material The online version of this article (10.1186/s13046-018-0840-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongshun Shi
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.,Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Hui Li
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key laboratory of ministry of education, Sun Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Ronghua Yuan
- Department of General Surgery, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001, China
| | - Wen Guan
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Xiaomei Zhang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Shaoyang Zhang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Wenliang Zhang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Fang Tong
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.,Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Li Li
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.,Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Zhihong Song
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China
| | - Changwei Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Shulan Yang
- Centre for Translational Medicine, the First Affiliated Hospital, SUN Yat-sen University, 58 Second Zhongshan Road, Guangzhou, 510080, China.
| | - Haihe Wang
- Department of Biochemistry, Zhongshan School of Medicine, SUN Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China. .,Center for Stem Cell Biology and Tissue Engineering, Key laboratory of ministry of education, Sun Yat-sen University, 74 Second Zhongshan Road, Guangzhou, 510080, China.
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45
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Specific binding of PCBP1 to heavily oxidized RNA to induce cell death. Proc Natl Acad Sci U S A 2018; 115:6715-6720. [PMID: 29891675 DOI: 10.1073/pnas.1806912115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In aerobically growing cells, the guanine base of RNA is oxidized to 8-oxo-7,8-dihydroguanine (8-oxoG), which induces alteration in their gene expression. We previously demonstrated that the human AUF1 protein binds to 8-oxoG in RNA to induce the selective degradation of oxidized messenger RNA. We herein report that the poly(C)-binding protein PCBP1 binds to more severely oxidized RNA to activate apoptosis-related reactions. While AUF1 binds to oligoribonucleotides carrying a single 8-oxoG, PCBP1 does not bind to such oligoribonucleotides but instead binds firmly to oligoribonucleotides in which two 8-oxoG residues are located nearby. PCBP1-deficient cells, constructed from the human HeLa S3 line using the CRISPR-Cas9 system, exhibited higher survival rates than HeLa S3 cells when small doses of hydrogen peroxide were applied. The levels of caspase-3 activation and PARP-1 cleavage in the PCBP1-deficient cells were significantly lower than those in wild-type cells. The structure-function relationship of PCBP1 was established with the use of PCBP1 mutant proteins in which the conserved KH domains were defective. Human cells appear to possess two distinct mechanisms, one controlled by AUF1 and the other by PCBP1, with the former functioning when messenger RNA is moderately oxidized and the latter operating when the RNA is more severely damaged.
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46
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Callow MG, Watanabe C, Wickliffe KE, Bainer R, Kummerfield S, Weng J, Cuellar T, Janakiraman V, Chen H, Chih B, Liang Y, Haley B, Newton K, Costa MR. CRISPR whole-genome screening identifies new necroptosis regulators and RIPK1 alternative splicing. Cell Death Dis 2018; 9:261. [PMID: 29449584 PMCID: PMC5833675 DOI: 10.1038/s41419-018-0301-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/04/2018] [Indexed: 12/04/2022]
Abstract
The necroptotic cell death pathway is a key component of human pathogen defense that can become aberrantly derepressed during tissue homeostasis to contribute to multiple types of tissue damage and disease. While formation of the necrosome kinase signaling complex containing RIPK1, RIPK3, and MLKL has been extensively characterized, additional mechanisms of its regulation and effector functions likely remain to be discovered. We screened 19,883 mouse protein-coding genes by CRISPR/Cas9-mediated gene knockout for resistance to cytokine-induced necroptosis and identified 112 regulators and mediators of necroptosis, including 59 new candidate pathway components with minimal or no effect on cell growth in the absence of necroptosis induction. Among these, we further characterized the function of PTBP1, an RNA binding protein whose activity is required to maintain RIPK1 protein abundance by regulating alternative splice-site selection.
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Affiliation(s)
- Marinella G Callow
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Colin Watanabe
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Katherine E Wickliffe
- Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Russell Bainer
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Sarah Kummerfield
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Julie Weng
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Trinna Cuellar
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | | | - Honglin Chen
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ben Chih
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yuxin Liang
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Michael R Costa
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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47
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Lubelsky Y, Ulitsky I. Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Nature 2018; 555:107-111. [PMID: 29466324 PMCID: PMC6047738 DOI: 10.1038/nature25757] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 12/29/2017] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as key parts of multiple cellular pathways, but their modes of action and how these are dictated by sequence remain unclear. lncRNAs tend to be enriched in the nuclear fraction, whereas most mRNAs are overtly cytoplasmic, although several studies have found that hundreds of mRNAs in various cell types are retained in the nucleus. It is thus conceivable that some mechanisms that promote nuclear enrichment are shared between lncRNAs and mRNAs. Here, to identify elements in lncRNAs and mRNAs that can force nuclear localization, we screened libraries of short fragments tiled across nuclear RNAs, which were cloned into the untranslated regions of an efficiently exported mRNA. The screen identified a short sequence derived from Alu elements and bound by HNRNPK that increased nuclear accumulation. Binding of HNRNPK to C-rich motifs outside Alu elements is also associated with nuclear enrichment in both lncRNAs and mRNAs, and this mechanism is conserved across species. Our results thus identify a pathway for regulation of RNA accumulation and subcellular localization that has been co-opted to regulate the fate of transcripts with integrated Alu elements.
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Affiliation(s)
- Yoav Lubelsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
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48
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Bogolyubov DS. Karyosphere (Karyosome): A Peculiar Structure of the Oocyte Nucleus. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 337:1-48. [PMID: 29551157 DOI: 10.1016/bs.ircmb.2017.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The karyosphere, aka the karyosome, is a meiosis-specific structure that represents a "knot" of condensed chromosomes joined together in a limited volume of the oocyte nucleus. The karyosphere is an evolutionarily conserved but morphologically rather "multifaceted" structure. It forms at the diplotene stage of meiotic prophase in many animals, from hydra and Drosophila to human. Karyosphere formation is generally linked with transcriptional silencing of the genome. It is believed that karyosphere/karyosome is a prerequisite for proper completion of meiotic divisions and further development. Here, a brief review on the karyosphere features in some invertebrates and vertebrates is provided. Special emphasis is made on terminology, since current discrepancies in this field may lead to confusions. In particular, it is proposed to distinguish the karyosphere with a capsule and the karyosome (a karyosphere devoid of a capsule). The "inverted" karyospheres are also considered, in which the chromosomes situate externally to an extrachromosomal structure (e.g., in human oocytes).
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Affiliation(s)
- Dmitry S Bogolyubov
- Institute of Cytology of the Russian Academy of Science, St. Petersburg, Russia.
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49
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Huang D, Lan W, Li D, Deng B, Lin W, Ren Y, Miao Y. WHIRLY1 Occupancy Affects Histone Lysine Modification and WRKY53 Transcription in Arabidopsis Developmental Manner. FRONTIERS IN PLANT SCIENCE 2018; 9:1503. [PMID: 30405658 PMCID: PMC6202938 DOI: 10.3389/fpls.2018.01503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 09/26/2018] [Indexed: 05/21/2023]
Abstract
Single-stranded DNA-binding proteins (SSBs) are assumed to involve in DNA replication, DNA repairmen, and gene transcription. Here, we provide the direct evidence on the functionality of an Arabidopsis SSB, WHIRLY1, by using loss- or gain-of-function lines. We show that WHIRLY1 binding to the promoter of WRKY53 represses the enrichment of H3K4me3, but enhances the enrichment of H3K9ac at the region contained WHIRLY1-binding sequences and TATA box or the translation start region of WRKY53, coincided with a recruitment of RNAPII. In vitro ChIP assays confirm that WHIRLY1 inhibits H3K4me3 enrichment at the preinitiation complex formation stage, while promotes H3K9ac enrichment and RNAPII recruitment at the elongation stage, consequently affecting the transcription of WRKY53. These results further explore the molecular actions underlying SSB-mediated gene transcription through epigenetic regulation in plant senescence.
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50
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Metabolic Pathways of the Warburg Effect in Health and Disease: Perspectives of Choice, Chain or Chance. Int J Mol Sci 2017; 18:ijms18122755. [PMID: 29257069 PMCID: PMC5751354 DOI: 10.3390/ijms18122755] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 12/13/2022] Open
Abstract
Focus on the Warburg effect, initially descriptive of increased glycolysis in cancer cells, has served to illuminate mitochondrial function in many other pathologies. This review explores our current understanding of the Warburg effect’s role in cancer, diabetes and ageing. We highlight how it can be regulated through a chain of oncogenic events, as a chosen response to impaired glucose metabolism or by chance acquisition of genetic changes associated with ageing. Such chain, choice or chance perspectives can be extended to help understand neurodegeneration, such as Alzheimer’s disease, providing clues with scope for therapeutic intervention. It is anticipated that exploration of Warburg effect pathways in extreme conditions, such as deep space, will provide further insights crucial for comprehending complex metabolic diseases, a frontier for medicine that remains equally significant for humanity in space and on earth.
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