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Göder A, Quinlan A, Rainey MD, Bennett D, Shamavu D, Corso J, Santocanale C. PTBP1 enforces ATR-CHK1 signaling determining the potency of CDC7 inhibitors. iScience 2023; 26:106951. [PMID: 37378325 PMCID: PMC10291475 DOI: 10.1016/j.isci.2023.106951] [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: 01/24/2023] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
CDC7 kinase is crucial for DNA replication initiation and fork processing. CDC7 inhibition mildly activates the ATR pathway, which further limits origin firing; however, to date the relationship between CDC7 and ATR remains controversial. We show that CDC7 and ATR inhibitors are either synergistic or antagonistic depending on the degree of inhibition of each individual kinase. We find that Polypyrimidine Tract Binding Protein 1 (PTBP1) is important for ATR activity in response to CDC7 inhibition and genotoxic agents. Compromised PTBP1 expression makes cells defective in RPA recruitment, genomically unstable, and resistant to CDC7 inhibitors. PTBP1 deficiency affects the expression and splicing of many genes indicating a multifactorial impact on drug response. We find that an exon skipping event in RAD51AP1 contributes to checkpoint deficiency in PTBP1-deficient cells. These results identify PTBP1 as a key factor in replication stress response and define how ATR activity modulates the activity of CDC7 inhibitors.
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Affiliation(s)
- Anja Göder
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Aisling Quinlan
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Michael D. Rainey
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Declan Bennett
- School of Mathematical & Statistical Sciences, University of Galway, Galway H91TK33, Ireland
| | - Daniel Shamavu
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Jacqueline Corso
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Corrado Santocanale
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
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2
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Chen XD, Liu HL, Li S, Hu KB, Wu QY, Liao P, Wang HY, Long ZY, Lu XM, Wang YT. The latest role of nerve-specific splicing factor PTBP1 in the transdifferentiation of glial cells into neurons. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1740. [PMID: 35574699 DOI: 10.1002/wrna.1740] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/16/2022] [Accepted: 04/21/2022] [Indexed: 11/07/2022]
Abstract
Central nervous system injury diseases can cause the loss of many neurons, and it is difficult to regenerate. The field of regenerative medicine believes that supplementing the missing neurons may be an ideal method for nerve injury repair. Recent studies have found that down-regulation of polypyrimidine tract binding protein 1 (PTBP1) expression can make glial cells transdifferentiate into different types of neurons, which is expected to be an alternative therapy to restore neuronal function. This article summarized the research progress on the structure and biological function of the PTBP family, the mutual regulation of PTBP1 and PTBP2, their role in neurogenesis, and the latest research progress in targeting PTBP1 to mediate the transdifferentiation of glial cells into neurons, which may provide some new strategies and new ideas for the future treatment of central nervous system injury and neurodegenerative diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Xing-Dong Chen
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China.,State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Hui-Lin Liu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Sen Li
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Kai-Bin Hu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Qing-Yun Wu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Ping Liao
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Hai-Yan Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Zai-Yun Long
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiu-Min Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Yong-Tang Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
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3
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Huang Q, Gu S, Fang J, Li X, Lin L. A pan-cancer analysis of the oncogenic role of polypyrimidine tract binding protein 1 (PTBP1) in human tumors. Medicine (Baltimore) 2022; 101:e32428. [PMID: 36595978 PMCID: PMC9803410 DOI: 10.1097/md.0000000000032428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Polypyrimidine tract-binding protein 1 (PTBP1) is an RNA-binding protein that regulates several posttranscriptional events and is closely related to the development of multiple tumors. However, little is known about PTBP1. Thus, we carried out a systematic pan-cancer analysis to explore the relationship between PTBP1 and cancer. METHODS We used The Cancer Genome Atlas, Gene Expression Omnibus, and Human Protein Atlas datasets, as well as several bioinformatics tools, to explore the role of PTBP1 in 33 tumor types. RESULTS The expression of PTBP1 in most tumor tissues was higher than that in normal tissues. Survival analysis indicated that overexpression of PTBP1 generally predicted poor overall survival in patients with tumors such as adrenocortical carcinoma, liver hepatocellular carcinoma, lung adenocarcinoma, and skin cutaneous melanoma. In addition, we compared the phosphorylation and immune infiltration of PTBP1 in cancer-associated fibroblasts between normal and primary tumor tissues and explored the putative functional mechanism of tumorigenesis mediated by PTBP1. CONCLUSION These results provide clues to better understand PTBP1 from the perspective of bioinformatics and highlight its importance in various human cancers.
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Affiliation(s)
- Qing Huang
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, P.R. China
| | - Shinong Gu
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, P.R. China
| | - Jianqi Fang
- Department of Women’s Health Care, Fujian Maternity and Child Health Hospital, Fuzhou, Fujian, P.R. China
| | - Xuanwen Li
- Graduate School of Health Science, Suzuka University of Medical Science, Suzuka, Mie, Japan
| | - Lili Lin
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, P.R. China
- * Correspondence: Lili Lin, College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian 361000, P.R. China (e-mail: )
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4
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Lan C, Zhang H, Wang K, Liu X, Zhao Y, Guo Z, Zhang N, Zhou Y, Gao M, Gu F, Ma Y. The alternative splicing of intersectin 1 regulated by PTBP1 promotes human glioma progression. Cell Death Dis 2022; 13:835. [PMID: 36171198 PMCID: PMC9519902 DOI: 10.1038/s41419-022-05238-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 01/23/2023]
Abstract
Intersectin 1 (ITSN1) contains two isoforms: ITSN1-S and ITSN1-L, which are highly regulated by alternative splicing. Our previous results showed that the two isoforms of ITSN1 displayed opposite functions: ITSN1-S promoted glioma development, while ITSN1-L exerted an inhibitory role in glioma progression. In this study, our transcriptome analysis using a large glioma cohort indicated that the ratio of ITSN1-S/ITSN1-L was positively correlated with glioma grading and poor prognosis. We identified the RNA-binding protein polypyrimidine tract-binding protein 1 (PTBP1) as an ITSN1 pre-mRNA interaction protein through RNA pull-down assay and RNA immunoprecipitation assay. Knockdown of PTBP1 decreased the ratio of ITSN1-S/ITSN1-L. Minigene reporter assay and mutation analyses further confirmed PTBP1 targeted polypyrimidine sequences on ITSN1 exon 30 (TTGCACTTCAGTATTTT) and promoted the inclusion of ITSN1 exon 30. Subsequently, silencing PTBP1 inhibited glioma cell proliferation, migration, and invasion by down-regulating the ratio of ITSN1-S/ITSN1-L. Taken together, our study provides a novel mechanism that PTBP1 modulates the alternative splicing of ITSN1 and promotes glioma proliferation and motility by up-regulating the ratio of ITSN1-S/ITSN1-L, thereby highlighting that PTBP1 may be an attractive therapeutic target for gliomas.
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Affiliation(s)
- Chungen Lan
- grid.411918.40000 0004 1798 6427Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Huikun Zhang
- grid.411918.40000 0004 1798 6427Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Kezhen Wang
- grid.411918.40000 0004 1798 6427Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Xiaoli Liu
- grid.411918.40000 0004 1798 6427Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Yawen Zhao
- grid.411918.40000 0004 1798 6427Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Zhifang Guo
- grid.411918.40000 0004 1798 6427Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Ning Zhang
- grid.411918.40000 0004 1798 6427Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Yongxia Zhou
- grid.411918.40000 0004 1798 6427Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Manzhi Gao
- grid.411918.40000 0004 1798 6427Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Feng Gu
- grid.411918.40000 0004 1798 6427Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Yongjie Ma
- grid.411918.40000 0004 1798 6427Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China ,grid.411918.40000 0004 1798 6427Tianjin’s Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China ,grid.411918.40000 0004 1798 6427Key Laboratory of Cancer Prevention and Therapy, Tianjin, China ,grid.265021.20000 0000 9792 1228Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
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5
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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6
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Pereira-Castro I, Moreira A. On the function and relevance of alternative 3'-UTRs in gene expression regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1653. [PMID: 33843145 DOI: 10.1002/wrna.1653] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022]
Abstract
Messanger RNA (mRNA) isoforms with alternative 3'-untranslated regions (3'-UTRs) are produced by alternative polyadenylation (APA), which occurs during transcription in most eukaryotic genes. APA fine-tunes gene expression in a cell-type- and cellular state-dependent manner. Selection of an APA site entails the binding of core cleavage and polyadenylation factors to a particular polyadenylation site localized in the pre-mRNA and is controlled by multiple regulatory determinants, including transcription, pre-mRNA cis-regulatory sequences, and protein factors. Alternative 3'-UTRs serve as platforms for specific RNA binding proteins and microRNAs, which regulate gene expression in a coordinated manner by controlling mRNA fate and function in the cell. Genome-wide studies illustrated the full extent of APA prevalence and revealed that specific 3'-UTR profiles are associated with particular cellular states and diseases. Generally, short 3'-UTRs are associated with proliferative and cancer cells, and long 3'-UTRs are mostly found in polarized and differentiated cells. Fundamental new insights on the physiological consequences of this widespread event and the molecular mechanisms involved have been revealed through single-cell studies. Publicly available comprehensive databases that cover all APA mRNA isoforms identified in many cellular states and diseases reveal specific APA signatures. Therapies tackling APA mRNA isoforms or APA regulators may be regarded as innovative and attractive tools for diagnostics or treatment of several pathologies. We highlight the function of APA and alternative 3'-UTRs in gene expression regulation, the control of these mechanisms, their physiological consequences, and their potential use as new biomarkers and therapeutic tools. This article is categorized under: RNA Processing > 3' End Processing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Isabel Pereira-Castro
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alexandra Moreira
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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7
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Kim W, Shin JC, Lee KH, Kim KT. PTBP1 Positively Regulates the Translation of Circadian Clock Gene, Period1. Int J Mol Sci 2020; 21:ijms21186921. [PMID: 32967200 PMCID: PMC7555454 DOI: 10.3390/ijms21186921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/19/2020] [Accepted: 09/19/2020] [Indexed: 11/16/2022] Open
Abstract
Circadian oscillations of mRNAs and proteins are the main features of circadian clock genes. Among them, Period1 (Per1) is a key component in negative-feedback regulation, which shows a robust diurnal oscillation and the importance of circadian rhythm and translational regulation of circadian clock genes has been recognized. In the present study, we investigated the 5'-untranslated region (5'-UTR) of the mouse core clock gene, Per1, at the posttranscriptional level, particularly its translational regulation. The 5'-UTR of Per1 was found to promote its translation via an internal ribosomal entry site (IRES). We found that polypyrimidine tract-binding protein 1 (PTBP1) binds to the 5'-UTR of Per1 and positively regulates the IRES-mediated translation of Per1 without affecting the levels of Per1 mRNA. The reduction of PTBP1 level also decreased the endogenous levels of the PER1 protein but not of its mRNA. As for the oscillation of PER1 expression, the disruption of PTBP1 levels lowered the PER1 expression but not the phase of the oscillation. PTBP1 also changed the amplitudes of the mRNAs of other circadian clock genes, such as Cryptochrome 1 (Cry1) and Per3. Our results suggest that the PTBP1 is important for rhythmic translation of Per1 and it fine-tunes the overall circadian system.
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Affiliation(s)
- Wanil Kim
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
| | | | - Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
- Correspondence: (K.-H.L.); (K.-T.K.); Tel.: +82-53-819-7743 (K.-H.L.); +82-54-279-2297 (K.-T.K.)
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology, Cheongam-Ro 77, Pohang, Gyeongbuk 37673, Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Cheongam-Ro 77, Pohang, Gyeongbuk 37673, Korea
- Correspondence: (K.-H.L.); (K.-T.K.); Tel.: +82-53-819-7743 (K.-H.L.); +82-54-279-2297 (K.-T.K.)
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8
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Moss ND, Sussel L. mRNA Processing: An Emerging Frontier in the Regulation of Pancreatic β Cell Function. Front Genet 2020; 11:983. [PMID: 33088281 PMCID: PMC7490333 DOI: 10.3389/fgene.2020.00983] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/03/2020] [Indexed: 01/04/2023] Open
Abstract
Robust endocrine cell function, particularly β cell function, is required to maintain blood glucose homeostasis. Diabetes can result from the loss or dysfunction of β cells. Despite decades of clinical and basic research, the precise regulation of β cell function and pathogenesis in diabetes remains incompletely understood. In this review, we highlight RNA processing of mRNAs as a rapidly emerging mechanism regulating β cell function and survival. RNA-binding proteins (RBPs) and RNA modifications are primed to be the next frontier to explain many of the poorly understood molecular processes that regulate β cell formation and function, and provide an exciting potential for the development of novel therapeutics. Here we outline the current understanding of β cell specific functions of several characterized RBPs, alternative splicing events, and transcriptome wide changes in RNA methylation. We also highlight several RBPs that are dysregulated in both Type 1 and Type 2 diabetes, and discuss remaining knowledge gaps in the field.
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Affiliation(s)
- Nicole D Moss
- Cell, Stem Cells, and Development Graduate Program, Department of Pediatrics, Barbara Davis Center, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, United States
| | - Lori Sussel
- Cell, Stem Cells, and Development Graduate Program, Department of Pediatrics, Barbara Davis Center, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, United States
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9
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Maris C, Jayne S, Damberger FF, Beusch I, Dorn G, Ravindranathan S, Allain FHT. A transient α-helix in the N-terminal RNA recognition motif of polypyrimidine tract binding protein senses RNA secondary structure. Nucleic Acids Res 2020; 48:4521-4537. [PMID: 32170319 PMCID: PMC7192611 DOI: 10.1093/nar/gkaa155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/22/2020] [Accepted: 03/04/2020] [Indexed: 12/14/2022] Open
Abstract
The polypyrimidine tract binding protein (PTB) is a multi-domain protein involved in alternative splicing, mRNA localization, stabilization, polyadenylation and translation initiation from internal ribosome entry sites (IRES). In this latter process, PTB promotes viral translation by interacting extensively with complex structured regions in the 5′-untranslated regions of viral RNAs at pyrimidine-rich targets located in single strand and hairpin regions. To better understand how PTB recognizes structured elements in RNA targets, we solved the solution structure of the N-terminal RNA recognition motif (RRM) in complex with an RNA hairpin embedding the loop sequence UCUUU, which is frequently found in IRESs of the picornovirus family. Surprisingly, a new three-turn α3 helix C-terminal to the RRM, folds upon binding the RNA hairpin. Although α3 does not mediate any contacts to the RNA, it acts as a sensor of RNA secondary structure, suggesting a role for RRM1 in detecting pyrimidine tracts in the context of structured RNA. Moreover, the degree of helix formation depends on the RNA loop sequence. Finally, we show that the α3 helix region, which is highly conserved in vertebrates, is crucial for PTB function in enhancing Encephalomyocarditis virus IRES activity.
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Affiliation(s)
| | - Sandrine Jayne
- Department of Biology, ETH Zurich, 8093 Zürich, Switzerland
| | | | - Irene Beusch
- Department of Biology, ETH Zurich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Department of Biology, ETH Zurich, 8093 Zürich, Switzerland
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10
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A three-dimensional bioprinted model to evaluate the effect of stiffness on neuroblastoma cell cluster dynamics and behavior. Sci Rep 2020; 10:6370. [PMID: 32286364 PMCID: PMC7156444 DOI: 10.1038/s41598-020-62986-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 03/19/2020] [Indexed: 12/20/2022] Open
Abstract
Three-dimensional (3D) bioprinted culture systems allow to accurately control microenvironment components and analyze their effects at cellular and tissue levels. The main objective of this study was to identify, quantify and localize the effects of physical-chemical communication signals between tumor cells and the surrounding biomaterial stiffness over time, defining how aggressiveness increases in SK-N-BE(2) neuroblastoma (NB) cell line. Biomimetic hydrogels with SK-N-BE(2) cells, methacrylated gelatin and increasing concentrations of methacrylated alginate (AlgMA 0%, 1% and 2%) were used. Young's modulus was used to define the stiffness of bioprinted hydrogels and NB tumors. Stained sections of paraffin-embedded hydrogels were digitally quantified. Human NB and 1% AlgMA hydrogels presented similar Young´s modulus mean, and orthotopic NB mice tumors were equally similar to 0% and 1% AlgMA hydrogels. Porosity increased over time; cell cluster density decreased over time and with stiffness, and cell cluster occupancy generally increased with time and decreased with stiffness. In addition, cell proliferation, mRNA metabolism and antiapoptotic activity advanced over time and with stiffness. Together, this rheological, optical and digital data show the potential of the 3D in vitro cell model described herein to infer how intercellular space stiffness patterns drive the clinical behavior associated with NB patients.
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11
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Sasanuma H, Ozawa M, Yoshida N. RNA-binding protein Ptbp1 is essential for BCR-mediated antibody production. Int Immunol 2020; 31:157-166. [PMID: 30476084 PMCID: PMC6400050 DOI: 10.1093/intimm/dxy077] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/21/2018] [Indexed: 11/22/2022] Open
Abstract
The RNA-binding protein polypyrimidine tract-binding protein-1 (Ptbp1) binds to the pyrimidine-rich sequence of target RNA and controls gene expression via post-transcriptional regulation such as alternative splicing. Although Ptbp1 is highly expressed in B lymphocytes, its role to date is largely unknown. To clarify the role of Ptbp1 in B-cell development and function, we generated B-cell-specific Ptbp1-deficient (P1BKO) mice. B-cell development in the bone marrow, spleen and peritoneal cavity of the P1BKO mice was nearly normal. However, the P1BKO mice had significantly lower levels of natural antibodies in serum compared with those of the control mice. To investigate the effect of Ptbp1 deficiency on the immune response in vivo, we immunized the P1BKO mice with T-cell-independent type-2 (TI-2) antigen NP-Ficoll and T-cell-dependent (TD) antigen NP-CGG. We found that B-cell-specific Ptbp1 deficiency causes an immunodeficiency phenotype due to defective production of antibody against both TI-2 and TD antigen. This immunodeficiency was accompanied by impaired B-cell receptor (BCR)-mediated B-cell activation and plasmablast generation. These findings demonstrate that Ptbp1 is essential for the humoral immune response.
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Affiliation(s)
- Hiroki Sasanuma
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
| | - Manabu Ozawa
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
| | - Nobuaki Yoshida
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
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12
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Ebrahimi D, Richards CM, Carpenter MA, Wang J, Ikeda T, Becker JT, Cheng AZ, McCann JL, Shaban NM, Salamango DJ, Starrett GJ, Lingappa JR, Yong J, Brown WL, Harris RS. Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease. Nat Commun 2018; 9:4137. [PMID: 30297863 PMCID: PMC6175962 DOI: 10.1038/s41467-018-06594-3] [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: 04/20/2018] [Accepted: 09/13/2018] [Indexed: 12/11/2022] Open
Abstract
Human APOBEC3H (A3H) is a single-stranded DNA cytosine deaminase that inhibits HIV-1. Seven haplotypes (I–VII) and four splice variants (SV154/182/183/200) with differing antiviral activities and geographic distributions have been described, but the genetic and mechanistic basis for variant expression and function remains unclear. Using a combined bioinformatic/experimental analysis, we find that SV200 expression is specific to haplotype II, which is primarily found in sub-Saharan Africa. The underlying genetic mechanism for differential mRNA splicing is an ancient intronic deletion [del(ctc)] within A3H haplotype II sequence. We show that SV200 is at least fourfold more HIV-1 restrictive than other A3H splice variants. To counteract this elevated antiviral activity, HIV-1 protease cleaves SV200 into a shorter, less restrictive isoform. Our analyses indicate that, in addition to Vif-mediated degradation, HIV-1 may use protease as a counter-defense mechanism against A3H in >80% of sub-Saharan African populations. Human APOBEC3H has several haplotypes and splice variants with distinct anti-HIV-1 activities, but the genetics underlying the expression of these variants are unclear. Here, the authors identify an intronic deletion in A3H haplotype II resulting in production of the most active splice variant, which is counteracted by HIV-1 protease.
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Affiliation(s)
- Diako Ebrahimi
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Christopher M Richards
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jiayi Wang
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Terumasa Ikeda
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jordan T Becker
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Adam Z Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Nadine M Shaban
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jairam R Lingappa
- Departments of Global Health, Medicine and Pediatrics, University of Washington, Seattle, WA, 98104, USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA. .,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
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13
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Singh R. RNA-protein interactions that regulate pre-mRNA splicing. Gene Expr 2018; 10:79-92. [PMID: 11868989 PMCID: PMC5977533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Splicing of nuclear precursor messenger RNAs is an important and ubiquitous type of gene regulation in metazoans. Splicing joins the coding sequences called exons by removing the intervening noncoding sequences, introns, from primary transcripts. Alternative splicing generates an enormous repertoire of functional diversity by producing multiple RNAs and proteins from a single gene. In fact, recent genome sequences from several organisms suggest that splicing regulation is likely to provide an important source of functional diversity in more complex organisms. Because splice sites are short sequences at the ends of introns, the functional splice sites have to be distinguished from an excessively large number of sequences in the primary transcripts that resemble a splice site. Furthermore, alternative splice sites have to be correctly chosen at appropriate times. Thus, selection of proper splice sites remains a daunting biological problem. This review focuses on a few examples in which the molecular and biochemical basis for splice site selection is better understood.
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Affiliation(s)
- Ravinder Singh
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, 80309, USA.
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14
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Suess B, Kemmerer K, Weigand JE. Splicing and Alternative Splicing Impact on Gene Design. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Beatrix Suess
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Katrin Kemmerer
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Julia E. Weigand
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
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15
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Liu W, Li X, Liao S, Dou K, Zhang Y. Activation of the intronic cryptic 5' splice site depends on its distance to the upstream cassette exon. Gene 2017; 619:30-36. [PMID: 28322992 DOI: 10.1016/j.gene.2017.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/13/2017] [Accepted: 03/17/2017] [Indexed: 11/30/2022]
Abstract
Splice site selection is a key step that determines the mRNA isoforms generated from a single transcript. The large diversity in splice site sequences emphasizes the plasticity of splice site recognition and selection. In this report, a cell-based reporter system using a SMN1/2 cassette exon was applied to study the roles governing the activation of a cryptic 5'SS from the intron 4 of the CT/CGRP gene. We found that the cryptic site was activated when placed within 124nt downstream the cassette exon, and the level of activation was negatively correlated with its distance from the exon. In addition, activation was not affected by PTB but was eliminated by an insertion extending the exon length. Activated cryptic 5'SSs in intron or exon could override the original alternative 5'SS, obeying the U1 base-pairing rule. These results suggest that the exon length itself could represent a factor in determining the splice site selection.
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Affiliation(s)
- Wei Liu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Xia Li
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Shengjie Liao
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China; Laboratory for Genome Regulation and Human Heath, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China
| | - Kefeng Dou
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China.
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China; Laboratory for Genome Regulation and Human Heath, ABLife Inc., Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, Hubei 430075, China.
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16
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He X, Yuan C, Yang J. Regulation and functional significance of CDC42 alternative splicing in ovarian cancer. Oncotarget 2016; 6:29651-63. [PMID: 26336992 PMCID: PMC4745753 DOI: 10.18632/oncotarget.4865] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 08/12/2015] [Indexed: 02/03/2023] Open
Abstract
Our previous study found that splicing factor polypyrimidine tract-binding protein 1 (PTBP1) had a role in tumorigenesis but the underlying mechanism remained unclear. In this study, we observed that knockdown of PTBP1 inhibited filopodia formation. Subsequently, we found that PTBP1 regulated the alternative splicing of CDC42, a major regulator of filopodia formation. Two CDC42 variants, CDC42-v1 and CDC42-v2, can be generated through alternative splicing. Knockdown of PTBP1 increased the expression of CDC42-v2. Ectopic expression of individual variants showed that CDC42-v2 suppressed filopodia formation, opposite to the effect of CDC42-v1. Quantitative RT-PCR revealed that CDC42-v2 was expressed at lower levels in ovarian cancer cell lines and ovarian tumor tissues than in normal control cells and tissues. Further, CDC42-v2 was observed to have inhibitory effects on ovarian tumor cell growth, colony formation in soft agar and invasiveness. In contrast, these inhibitory effects were not found with CDC42-v1. Taken together, above results suggest that the role of PTBP1 in tumorigenesis may be partly mediated by its regulation of CDC42 alternative splicing and CDC42-v2 might function as a tumor suppressor.
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Affiliation(s)
- Xiaolong He
- Department of Biopharmaceutical Sciences, College of Pharmacy-Rockford, The University of Illinois at Chicago, Rockford, IL 61107, USA
| | - Chengfu Yuan
- Medical College of China Three Gorges University, Yichang, Hubei, 443002, People's Republic of China
| | - Jilai Yang
- Department of Biopharmaceutical Sciences, College of Pharmacy-Rockford, The University of Illinois at Chicago, Rockford, IL 61107, USA
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17
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Domingues RG, Lago-Baldaia I, Pereira-Castro I, Fachini JM, Oliveira L, Drpic D, Lopes N, Henriques T, Neilson JR, Carmo AM, Moreira A. CD5 expression is regulated during human T-cell activation by alternative polyadenylation, PTBP1, and miR-204. Eur J Immunol 2016; 46:1490-503. [PMID: 27005442 DOI: 10.1002/eji.201545663] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 02/17/2016] [Accepted: 03/16/2016] [Indexed: 01/29/2023]
Abstract
T lymphocytes stimulated through their antigen receptor (TCR) preferentially express mRNA isoforms with shorter 3´ untranslated regions (3´-UTRs) derived from alternative pre-mRNA cleavage and polyadenylation (APA). However, the physiological relevance of APA programs remains poorly understood. CD5 is a T-cell surface glycoprotein that negatively regulates TCR signaling from the onset of T-cell activation. CD5 plays a pivotal role in mediating outcomes of cell survival or apoptosis, and may prevent both autoimmunity and cancer. In human primary T lymphocytes and Jurkat cells we found three distinct mRNA isoforms encoding CD5, each derived from distinct poly(A) signals (PASs). Upon T-cell activation, there is an overall increase in CD5 mRNAs with a specific increase in the relative expression of the shorter isoforms. 3´-UTRs derived from these shorter isoforms confer higher reporter expression in activated T cells relative to the longer isoform. We further show that polypyrimidine tract binding protein (PTB/PTBP1) directly binds to the proximal PAS and PTB siRNA depletion causes a decrease in mRNA derived from this PAS, suggesting an effect on stability or poly(A) site selection to circumvent targeting of the longer CD5 mRNA isoform by miR-204. These mechanisms fine-tune CD5 expression levels and thus ultimately T-cell responses.
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Affiliation(s)
- Rita G Domingues
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Inês Lago-Baldaia
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Isabel Pereira-Castro
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Joseph M Fachini
- Department of Molecular Physiology and Biophysics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Liliana Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Cell Activation and Gene Expression Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Danica Drpic
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Nair Lopes
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Telmo Henriques
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Alexandre M Carmo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Cell Activation and Gene Expression Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Alexandra Moreira
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
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18
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Takahashi H, Nishimura J, Kagawa Y, Kano Y, Takahashi Y, Wu X, Hiraki M, Hamabe A, Konno M, Haraguchi N, Takemasa I, Mizushima T, Ishii M, Mimori K, Ishii H, Doki Y, Mori M, Yamamoto H. Significance of Polypyrimidine Tract–Binding Protein 1 Expression in Colorectal Cancer. Mol Cancer Ther 2015; 14:1705-16. [DOI: 10.1158/1535-7163.mct-14-0142] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/12/2015] [Indexed: 11/16/2022]
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19
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Abstract
The spliceosomal factor TRAP150 is essential for pre-mRNA splicing in vivo and, when overexpressed, it enhances splicing efficiency. In this study, we found that TRAP150 interacted with the cleavage and polyadenylation specificity factor (CPSF) and co-fractionated with CPSF and RNA polymerase II. Moreover, TRAP150 preferentially associated with the U1 small ribonucleoprotein (snRNP). However, our data do not support a role for TRAP150 in alternative 5′ splice site or exon selection or in alternative polyadenylation. Because U1 snRNP participates in premature cleavage and polyadenylation (PCPA), we tested whether TRAP150 is a cofactor in the control of PCPA. Although TRAP150 depletion had no significant effect on PCPA, overexpression of TRAP150 forced activation of a cryptic 3′ splice site, yielding spliced PCPA transcripts. Mechanistic studies showed that TRAP150-activated splicing occurred in composite but not authentic terminal exons, and such an activity was enhanced by debilitation of U1 snRNP or interference with transcription elongation or termination. Together, these results indicate that TRAP150 provides an additional layer of PCPA regulation, through which it may increase the diversity of abortive RNA transcripts under conditions of compromised gene expression.
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Affiliation(s)
- Kuo-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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20
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PTBP1 is required for glucose-stimulated cap-independent translation of insulin granule proteins and Coxsackieviruses in beta cells. Mol Metab 2014; 3:518-30. [PMID: 25061557 PMCID: PMC4099505 DOI: 10.1016/j.molmet.2014.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/02/2014] [Accepted: 05/06/2014] [Indexed: 12/15/2022] Open
Abstract
Glucose and GLP-1 stimulate not only insulin secretion, but also the post-transcriptional induction of insulin granule biogenesis. This process involves the nucleocytoplasmic translocation of the RNA binding protein PTBP1. Binding of PTBP1 to the 3'-UTRs of mRNAs for insulin and other cargoes of beta cell granules increases their stability. Here we show that glucose enhances also the binding of PTBP1 to the 5'-UTRs of these transcripts, which display IRES activity, and their translation exclusively in a cap-independent fashion. Accordingly, glucose-induced biosynthesis of granule cargoes was unaffected by pharmacological, genetic or Coxsackievirus-mediated inhibition of cap-dependent translation. Infection with Coxsackieviruses, which also depend on PTBP1 for their own cap-independent translation, reduced instead granule stores and insulin release. These findings provide insight into the mechanism for glucose-induction of insulin granule production and on how Coxsackieviruses, which have been implicated in the pathogenesis of type 1 diabetes, can foster beta cell failure.
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Key Words
- Beta cells
- CV, Coxsackievirus
- Diabetes
- ER, endoplasmic reticulum
- EV, Enterovirus
- F, Faulkner
- FL, firefly luciferase
- IRES, internal ribosomal entry site
- ITAF, IRES-trans-acting factor
- Insulin
- MCA, MIN6 cell adapted
- PABP, poly(A)-binding protein
- PC, prohormone convertase
- PTBP1, polypyrimidine tract-binding protein 1
- Polypyrimidine tract-binding protein
- S6K1, p70S6 Kinase 1
- Secretory granules
- T1D, type 1 diabetes
- Translation
- UTR, untranslated region
- Virus
- eIF4E-V5, eIF4E tagged at its C-terminus with a V5-epitope
- mTORC1, mammalian Target Of Rapamycin Complex 1
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21
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New insights into functional roles of the polypyrimidine tract-binding protein. Int J Mol Sci 2013; 14:22906-32. [PMID: 24264039 PMCID: PMC3856098 DOI: 10.3390/ijms141122906] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 11/13/2013] [Accepted: 11/13/2013] [Indexed: 12/20/2022] Open
Abstract
Polypyrimidine Tract Binding Protein (PTB) is an intensely studied RNA binding protein involved in several post-transcriptional regulatory events of gene expression. Initially described as a pre-mRNA splicing regulator, PTB is now widely accepted as a multifunctional protein shuttling between nucleus and cytoplasm. Accordingly, PTB can interact with selected RNA targets, structural elements and proteins. There is increasing evidence that PTB and its paralog PTBP2 play a major role as repressors of alternatively spliced exons, whose transcription is tissue-regulated. In addition to alternative splicing, PTB is involved in almost all steps of mRNA metabolism, including polyadenylation, mRNA stability and initiation of protein translation. Furthermore, it is well established that PTB recruitment in internal ribosome entry site (IRES) activates the translation of picornaviral and cellular proteins. Detailed studies of the structural properties of PTB have contributed to our understanding of the mechanism of RNA binding by RNA Recognition Motif (RRM) domains. In the present review, we will describe the structural properties of PTB, its paralogs and co-factors, the role in post-transcriptional regulation and actions in cell differentiation and pathogenesis. Defining the multifunctional roles of PTB will contribute to the understanding of key regulatory events in gene expression.
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22
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McDermott SM, Davis I. Drosophila Hephaestus/polypyrimidine tract binding protein is required for dorso-ventral patterning and regulation of signalling between the germline and soma. PLoS One 2013; 8:e69978. [PMID: 23894566 PMCID: PMC3720928 DOI: 10.1371/journal.pone.0069978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/14/2013] [Indexed: 02/05/2023] Open
Abstract
In the Drosophila oocyte, gurken (grk) mRNA encodes a secreted TGF-α signal that specifies the future embryonic dorso-ventral axes by altering the fate of the surrounding epithelial follicle cells. We previously identified a number of RNA binding proteins that associate specifically with the 64 nucleotide grk localization signal, including the Drosophila orthologue of polypyrimidine tract-binding protein (PTB), Hephaestus (Heph). To test whether Heph is required for correct grk mRNA or protein function, we used immunoprecipitation to validate the association of Heph with grk mRNA and characterized the heph mutant phenotype. We found that Heph is a component of grk mRNP complexes but heph germline clones show that Heph is not required for grk mRNA localization. Instead, we identify a novel function for Heph in the germline and show that it is required for proper Grk protein localization. Furthermore, we show that Heph is required in the oocyte for the correct organization of the actin cytoskeleton and dorsal appendage morphogenesis. Our results highlight a requirement for an mRNA binding protein in the localization of Grk protein, which is independent of mRNA localization, and we propose that Heph is required in the germline for efficient Grk signalling to the somatic follicle cells during dorso-ventral patterning.
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Affiliation(s)
- Suzanne M. McDermott
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (SMM); (ID)
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (SMM); (ID)
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23
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Abstract
The perinucleolar compartment (PNC) is a unique nuclear substructure, forming predominantly in cancer cells both in vitro and in vivo. PNC prevalence (percentage of cells containing at least one PNC) has been found to positively correlate with disease progression in several cancers (breast, ovarian, and colon). While there is a clear association between PNCs and cancer, the molecular function of the PNC remains unclear. Here we summarize the current understanding of the association of PNCs with cancer and its possible functions in cancer cells.
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Affiliation(s)
- Yiping Wen
- Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, IL 60611, USA ; College of Veterinary Medicine, Sichuan Agricultural University, Yaan 625014, China
| | - Chen Wang
- Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, IL 60611, USA
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, IL 60611, USA
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24
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Costessi L, Porro F, Iaconcig A, Nedeljkovic M, Muro AF. Characterization of the distal polyadenylation site of the ß-adducin (Add2) pre-mRNA. PLoS One 2013; 8:e58879. [PMID: 23554949 PMCID: PMC3598803 DOI: 10.1371/journal.pone.0058879] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/07/2013] [Indexed: 12/05/2022] Open
Abstract
Most genes have multiple polyadenylation sites (PAS), which are often selected in a tissue-specific manner, altering protein products and affecting mRNA stability, subcellular localization and/or translability. Here we studied the polyadenylation mechanisms associated to the beta-adducin gene (Add2). We have previously shown that the Add2 gene has a very tight regulation of alternative polyadenylation, using proximal PAS in erythroid tissues, and a distal one in brain. Using chimeric minigenes and cell transfections we identified the core elements responsible for polyadenylation at the distal PAS. Deletion of either the hexanucleotide motif (Hm) or the downstream element (DSE) resulted in reduction of mature mRNA levels and activation of cryptic PAS, suggesting an important role for the DSE in polyadenylation of the distal Add2 PAS. Point mutation of the UG repeats present in the DSE, located immediately after the cleavage site, resulted in a reduction of processed mRNA and in the activation of the same cryptic site. RNA-EMSA showed that this region is active in forming RNA-protein complexes. Competition experiments showed that RNA lacking the DSE was not able to compete the RNA-protein complexes, supporting the hypothesis of an essential important role for the DSE. Next, using a RNA-pull down approach we identified some of the proteins bound to the DSE. Among these proteins we found PTB, TDP-43, FBP1 and FBP2, nucleolin, RNA helicase A and vigilin. All these proteins have a role in RNA metabolism, but only PTB has a reported function in polyadenylation. Additional experiments are needed to determine the precise functional role of these proteins in Add2 polyadenylation.
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Affiliation(s)
- Luisa Costessi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Fabiola Porro
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Alessandra Iaconcig
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Mirjana Nedeljkovic
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Andrés Fernando Muro
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- * E-mail:
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25
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Izaguirre DI, Zhu W, Hai T, Cheung HC, Krahe R, Cote GJ. PTBP1-dependent regulation of USP5 alternative RNA splicing plays a role in glioblastoma tumorigenesis. Mol Carcinog 2012; 51:895-906. [PMID: 21976412 PMCID: PMC3319169 DOI: 10.1002/mc.20859] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 06/21/2011] [Accepted: 09/08/2011] [Indexed: 11/08/2022]
Abstract
Aberrant RNA splicing is thought to play a key role in tumorigenesis. The assessment of its specific contributions is limited by the complexity of information derived from genome-wide array-based approaches. We describe how performing splicing factor-specific comparisons using both tumor and cell line data sets may more readily identify physiologically relevant tumor-specific splicing events. Affymetrix exon array data derived from glioblastoma (GBM) tumor samples with defined polypyrimidine tract-binding protein 1 (PTBP1) levels were compared with data from U251 GBM cells with and without PTBP1 knockdown. This comparison yielded overlapping gene sets that comprised only a minor fraction of each data set. The identification of a novel GBM-specific splicing event involving the USP5 gene led us to further examine its role in tumorigenesis. In GBM, USP5 generates a shorter isoform 2 through recognition of a 5' splice site within exon 15. Production of the USP5 isoform 2 was strongly correlated with PTBP1 expression in GBM tumor samples and cell lines. Splicing regulation was consistent with the presence of an intronic PTBP1 binding site and could be modulated through antisense targeting of the isoform 2 splice site to force expression of isoform 1 in GBM cells. The forced expression of USP5 isoform 1 in two GBM cell lines inhibited cell growth and migration, implying an important role for USP5 splicing in gliomagenesis. These results support a role for aberrant RNA splicing in tumorigenesis and suggest that changes in relatively few genes may be sufficient to drive the process.
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Affiliation(s)
- Daisy I. Izaguirre
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas
- The University of Texas Graduate School of Biomedical Sciences, Houston, Texas
| | - Wen Zhu
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tao Hai
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hannah C. Cheung
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas
- The University of Texas Graduate School of Biomedical Sciences, Houston, Texas
| | - Ralf Krahe
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- The University of Texas Graduate School of Biomedical Sciences, Houston, Texas
| | - Gilbert J. Cote
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas
- The University of Texas Graduate School of Biomedical Sciences, Houston, Texas
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26
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Keppetipola N, Sharma S, Li Q, Black DL. Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2. Crit Rev Biochem Mol Biol 2012; 47:360-78. [PMID: 22655688 DOI: 10.3109/10409238.2012.691456] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Alternative splicing patterns are regulated by RNA binding proteins that assemble onto each pre-mRNA to form a complex RNP structure. The polypyrimidine tract binding protein, PTB, has served as an informative model for understanding how RNA binding proteins affect spliceosome assembly and how changes in the expression of these proteins can control complex programs of splicing in tissues. In this review, we describe the mechanisms of splicing regulation by PTB and its function, along with its paralog PTBP2, in neuronal development.
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Affiliation(s)
- Niroshika Keppetipola
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
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27
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Engels B, Jannot G, Remenyi J, Simard MJ, Hutvagner G. Polypyrimidine tract binding protein (hnRNP I) is possibly a conserved modulator of miRNA-mediated gene regulation. PLoS One 2012; 7:e33144. [PMID: 22427970 PMCID: PMC3302860 DOI: 10.1371/journal.pone.0033144] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 02/10/2012] [Indexed: 11/19/2022] Open
Abstract
MiRNAs can regulate gene expression through versatile mechanisms that result in increased or decreased expression of the targeted mRNA and it could effect the expression of thousands of protein in a particular cell. An increasing body of evidence suggest that miRNAs action can be modulated by proteins that bind to the same 3′UTRs that are targeted by miRNAs, suggesting that other factors apart from miRNAs and their target sites determine miRNA-modulation of gene expression. We applied an affinity purification protocol using biotinylated let-7 miRNA inhibitor to isolate proteins that are involved in let-7 mediated gene regulation that resulted in an affinity purification of Polypyrimidine Tract Binding protein (PTB). Here we show that PTB interacts with miRNAs and human Argonaute 2 (hAgo2) through RNA as well as identified potential mammalian cellular targets that are co-regulated by PTB and hAgo2. In addition, using genetic approach, we have demonstrated that PTB genetically interacts with Caenorhabditis elegans let-7 indicating a conserved role for PTB in miRNA-mediated gene regulation.
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Affiliation(s)
- Bart Engels
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Guillaume Jannot
- Laval University Cancer Research Centre, Hôtel-Dieu de Québec (CHUQ), Québec City, Québec, Canada
| | - Judit Remenyi
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Martin J. Simard
- Laval University Cancer Research Centre, Hôtel-Dieu de Québec (CHUQ), Québec City, Québec, Canada
| | - György Hutvagner
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- Centre for Health Technologies, University of Technology, Sydney, Sydney, Australia
- * E-mail:
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28
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Wachter A, Rühl C, Stauffer E. The Role of Polypyrimidine Tract-Binding Proteins and Other hnRNP Proteins in Plant Splicing Regulation. FRONTIERS IN PLANT SCIENCE 2012; 3:81. [PMID: 22639666 PMCID: PMC3355609 DOI: 10.3389/fpls.2012.00081] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 04/11/2012] [Indexed: 05/18/2023]
Abstract
Alternative precursor mRNA splicing is a widespread phenomenon in multicellular eukaryotes and represents a major means for functional expansion of the transcriptome. While several recent studies have revealed an important link between splicing regulation and fundamental biological processes in plants, many important aspects, such as the underlying splicing regulatory mechanisms, are so far not well understood. Splicing decisions are in general based on a splicing code that is determined by the dynamic interplay of splicing-controlling factors and cis-regulatory elements. Several members of the group of heterogeneous nuclear ribonucleoprotein (hnRNP) proteins are well known regulators of splicing in animals and the comparatively few reports on some of their plant homologs revealed similar functions. This also applies to polypyrimidine tract-binding proteins, a thoroughly investigated class of hnRNP proteins with splicing regulatory functions in both animals and plants. Further examples from plants are auto- and cross-regulatory splicing circuits of glycine-rich RNA binding proteins and splicing enhancement by oligouridylate binding proteins. Besides their role in defining splice site choice, hnRNP proteins are also involved in multiple other steps of nucleic acid metabolism, highlighting the functional versatility of this group of proteins in higher eukaryotes.
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Affiliation(s)
- Andreas Wachter
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
- *Correspondence: Andreas Wachter, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany. e-mail:
| | - Christina Rühl
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
| | - Eva Stauffer
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
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29
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Shen M, Mattox W. Activation and repression functions of an SR splicing regulator depend on exonic versus intronic-binding position. Nucleic Acids Res 2011; 40:428-37. [PMID: 21914724 PMCID: PMC3245930 DOI: 10.1093/nar/gkr713] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
SR proteins and related factors play widespread roles in alternative pre-mRNA splicing and are known to promote splice site recognition through their Arg–Ser-rich effector domains. However, binding of SR regulators to some targets results in repression of splice sites through a distinct mechanism. Here, we investigate how activated and repressed targets of the Drosophila SR regulator Transformer2 elicit its differing effects on splicing. We find that, like activation, repression affects early steps in the recognition of splice sites and spliceosome assembly. Repositioning of regulatory elements reveals that Tra2 complexes that normally repress splicing from intronic positions activate splicing when located in an exon. Protein tethering experiments demonstrate that this position dependence is an intrinsic property of Tra2 and further show that repression and activation are mediated by separate effector domains of this protein. When other Drosophila SR factors (SF2 and Rbp1) that activate splicing from exonic positions were tethered intronically they failed to either activate or repress splicing. Interestingly, both activities of Tra2 favor the exonic identity of the RNA sequences that encompass its binding sites. This suggests a model in which these two opposite functions act in concert to define both the position and extent of alternatively spliced exons.
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Affiliation(s)
- Manli Shen
- Department of Genetics and Genes & Development Graduate Program, University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
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30
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Sharma S, Maris C, Allain FHT, Black DL. U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression. Mol Cell 2011; 41:579-88. [PMID: 21362553 DOI: 10.1016/j.molcel.2011.02.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 12/08/2010] [Accepted: 01/07/2011] [Indexed: 11/17/2022]
Abstract
Splicing of the c-src N1 exon is repressed by the polypyrimidine tract-binding protein (PTB or PTBP1). During exon repression, the U1 snRNP binds properly to the N1 exon 5' splice site but is made inactive by the presence of PTB. Examining the patterns of nuclease protection at this 5' splice site, we find that the interaction of U1 is altered by the adjacent PTB. Interestingly, UV crosslinking identifies a direct contact between the pre-mRNA-bound PTB and the U1 snRNA. EMSA, ITC, and NMR studies show that PTB RRMs 1 and 2 bind the pyrimidine-rich internal loop of U1 snRNA stem loop 4. The PTB/U1 interaction prevents further assembly of the U1 snRNP with spliceosomal components downstream. This precise interaction between a splicing regulator and an snRNA component of the spliceosome points to a range of different mechanisms for splicing regulation.
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Affiliation(s)
- Shalini Sharma
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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31
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He X, Arslan AD, Pool MD, Ho TT, Darcy KM, Coon JS, Beck WT. Knockdown of splicing factor SRp20 causes apoptosis in ovarian cancer cells and its expression is associated with malignancy of epithelial ovarian cancer. Oncogene 2010; 30:356-65. [PMID: 20856201 PMCID: PMC3010329 DOI: 10.1038/onc.2010.426] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Our previous study revealed that two splicing factors, polypyrimidine tract-binding protein (PTB) and SRp20, were up-regulated in epithelial ovarian cancer (EOC) and knockdown of PTB expression inhibited ovarian tumor cell growth and transformation properties. In this report, we show that knockdown of SRp20 expression in ovarian cancer cells also causes substantial inhibition of tumor cell growth and colony formation in soft agar and the extent of such inhibition appeared to correlate with the extent of suppression of SRp20. Massive knockdown of SRp20 expression triggered remarkable apoptosis in these cells. These results suggest that overexpression of SRp20 is required for ovarian tumor cell growth and survival. Immunohistochemical staining for PTB and SRp20 of two specialized tissue microarrays (TMAs), one containing benign ovarian tumors, borderline/low malignant potential (LMP) ovarian tumors as well as invasive EOC and the other containing invasive EOC ranging from stage I to stage IV disease, reveals that PTB and SRp20 are both expressed differentially between benign tumors and invasive EOC, and between borderline/LMP tumors and invasive EOC. There were more all-negative or mixed staining cases (at least two evaluable section cores per case) in benign tumors than in invasive EOC while there were more all positive staining cases in invasive EOC than in the other two disease classifications. Among invasive EOC, the great majority of cases were stained all-positive for both PTB and SRp20 and there were no significant differences in average staining or frequency of positive cancer cells between any of the tumor stages. Therefore, the expression of PTB and SRp20 is associated with malignancy of ovarian tumors but not with stage of invasive EOC.
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Affiliation(s)
- X He
- Department of Biopharmaceutical Sciences, College of Pharmacy and Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA.
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32
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Llorian M, Schwartz S, Clark TA, Hollander D, Tan LY, Spellman R, Gordon A, Schweitzer AC, de la Grange P, Ast G, Smith CWJ. Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB. Nat Struct Mol Biol 2010; 17:1114-23. [PMID: 20711188 PMCID: PMC2933513 DOI: 10.1038/nsmb.1881] [Citation(s) in RCA: 200] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 06/25/2010] [Indexed: 12/22/2022]
Abstract
To gain global insights into the role of the well-known repressive splicing regulator PTB, we analyzed the consequences of PTB knockdown in HeLa cells using high-density oligonucleotide splice-sensitive microarrays. The major class of identified PTB-regulated splicing event was PTB-repressed cassette exons, but there was also a substantial number of PTB-activated splicing events. PTB-repressed and PTB-activated exons showed a distinct arrangement of motifs with pyrimidine-rich motif enrichment within and upstream of repressed exons but downstream of activated exons. The N-terminal half of PTB was sufficient to activate splicing when recruited downstream of a PTB-activated exon. Moreover, insertion of an upstream pyrimidine tract was sufficient to convert a PTB-activated exon to a PTB-repressed exon. Our results show that PTB, an archetypal splicing repressor, has variable splicing activity that predictably depends upon its binding location with respect to target exons.
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Affiliation(s)
- Miriam Llorian
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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33
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RNA looping by PTB: Evidence using FRET and NMR spectroscopy for a role in splicing repression. Proc Natl Acad Sci U S A 2010; 107:4105-10. [PMID: 20160105 DOI: 10.1073/pnas.0907072107] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing plays an important role in generating proteome diversity. The polypyrimidine tract-binding protein (PTB) is a key alternative splicing factor involved in exon repression. It has been proposed that PTB acts by looping out exons flanked by pyrimidine tracts. We present fluorescence, NMR, and in vivo splicing data in support of a role of PTB in inducing RNA loops. We show that the RNA recognition motifs (RRMs) 3 and 4 of PTB can bind two distant pyrimidine tracts and bring their 5' and 3' ends in close proximity, thus looping the RNA. Efficient looping requires an intervening sequence of 15 nucleotides or longer between the pyrimidine tracts. RRM3 and RRM4 bind the 5' and the 3' pyrimidine tracts, respectively, in a specific directionality and work synergistically for efficient splicing repression in vivo.
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34
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Millevoi S, Vagner S. Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation. Nucleic Acids Res 2009; 38:2757-74. [PMID: 20044349 PMCID: PMC2874999 DOI: 10.1093/nar/gkp1176] [Citation(s) in RCA: 291] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Messenger RNA (mRNA) 3′ end formation is a nuclear process through which all eukaryotic primary transcripts are endonucleolytically cleaved and most of them acquire a poly(A) tail. This process, which consists in the recognition of defined poly(A) signals of the pre-mRNAs by a large cleavage/polyadenylation machinery, plays a critical role in gene expression. Indeed, the poly(A) tail of a mature mRNA is essential for its functions, including stability, translocation to the cytoplasm and translation. In addition, this process serves as a bridge in the network connecting the different transcription, capping, splicing and export machineries. It also participates in the quantitative and qualitative regulation of gene expression in a variety of biological processes through the selection of single or alternative poly(A) signals in transcription units. A large number of protein factors associates with this machinery to regulate the efficiency and specificity of this process and to mediate its interaction with other nuclear events. Here, we review the eukaryotic 3′ end processing machineries as well as the comprehensive set of regulatory factors and discuss the different molecular mechanisms of 3′ end processing regulation by proposing several overlapping models of regulation.
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Affiliation(s)
- Stefania Millevoi
- Institut National de la Santé et de la Recherche Médicale U563, Toulouse, F-31000, France.
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35
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Abstract
In cells responding to low oxygen levels, gene expression patterns are strongly influenced by post-transcriptional processes. RNA-binding proteins (RBPs) are pivotal regulators of gene expression in response to numerous stresses, including hypoxia. Here, we review the RBPs that modulate mRNA turnover and translation in response to hypoxic challenge. The RBPs HuR (human antigen R) and PTB (polypyrimidine tract-binding protein) associate with mRNAs encoding hypoxia-response proteins such as HIF-1α and VEGF mRNAs, enhance their expression after hypoxia and play a major role in establishing hypoxic gene expression patterns. Additional RBPs such as iron-response element-binding proteins (IRPs), cytoplasmic polyadenylation-element-binding proteins (CPEBs) and several heterogeneous nuclear ribonucleoproteins (hnRNPs) also bind to hypoxia-regulated transcripts and modulate the levels of the encoded proteins. We discuss the efficient regulation of hypoxic gene expression by RBPs and the mounting interest in targeting hypoxia-regulatory RBPs in diseases with aberrant hypoxic responses.
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Affiliation(s)
- Kiyoshi Masuda
- Laboratory of Cellular and Molecular Biology, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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Roles of polypyrimidine tract binding proteins in major immediate-early gene expression and viral replication of human cytomegalovirus. J Virol 2009; 83:2839-50. [PMID: 19144709 DOI: 10.1128/jvi.02407-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Human cytomegalovirus (HCMV), a member of the beta subgroup of the family Herpesviridae, causes serious health problems worldwide. HCMV gene expression in host cells is a well-defined sequential process: immediate-early (IE) gene expression, early-gene expression, DNA replication, and late-gene expression. The most abundant IE gene, major IE (MIE) gene pre-mRNA, needs to be spliced before being exported to the cytoplasm for translation. In this study, the regulation of MIE gene splicing was investigated; in so doing, we found that polypyrimidine tract binding proteins (PTBs) strongly repressed MIE gene production in cotransfection assays. In addition, we discovered that the repressive effects of PTB could be rescued by splicing factor U2AF. Taken together, the results suggest that PTBs inhibit MIE gene splicing by competing with U2AF65 for binding to the polypyrimidine tract in pre-mRNA. In intron deletion mutation assays and RNA detection experiments (reverse transcription [RT]-PCR and real-time RT-PCR), we further observed that PTBs target all the introns of the MIE gene, especially intron 2, and affect gene splicing, which was reflected in the variation in the ratio of pre-mRNA to mRNA. Using transfection assays, we demonstrated that PTB knockdown cells induce a higher degree of MIE gene splicing/expression. Consistently, HCMV can produce more viral proteins and viral particles in PTB knockdown cells after infection. We conclude that PTB inhibits HCMV replication by interfering with MIE gene splicing through competition with U2AF for binding to the polypyrimidine tract in MIE gene introns.
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37
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Raponi M, Buratti E, Llorian M, Stuani C, Smith CWJ, Baralle D. Polypyrimidine tract binding protein regulates alternative splicing of an aberrant pseudoexon in NF1. FEBS J 2008; 275:6101-8. [PMID: 19016857 DOI: 10.1111/j.1742-4658.2008.06734.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In disease-associated genes, understanding the functional significance of deep intronic nucleotide variants represents a difficult challenge. We previously reported that an NF1 intron 30 exonization event is triggered from a single correct nomenclature is 'c.293-279 A>G' mutation [Raponi M, Upadhyaya M & Baralle D (2006) Hum Mutat 27, 294-295]. In this paper, we investigate which characteristics play a role in regulating inclusion of the aberrant pseudoexon. Our investigation shows that pseudoexon inclusion levels are strongly downregulated by polypyrimidine tract binding protein and its homologue neuronal polypyrimidine tract binding protein. In particular, we provide evidence that the functional effect of polypyrimidine tract binding protein is proportional to its concentration, and map the cis-acting elements that are principally responsible for this negative regulation. These results highlight the importance of evaluating local sequence context for diagnostic purposes, and the utility of developing therapies to turn off activated pseudoexons.
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38
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Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein. Biochem Soc Trans 2008; 36:641-7. [PMID: 18631133 DOI: 10.1042/bst0360641] [Citation(s) in RCA: 240] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PTB (polypyrimidine-tract-binding protein) is a ubiquitous RNA-binding protein. It was originally identified as a protein with a role in splicing but it is now known to function in a large number of diverse cellular processes including polyadenylation, mRNA stability and translation initiation. Specificity of PTB function is achieved by a combination of changes in the cellular localization of this protein (its ability to shuttle from the nucleus to the cytoplasm is tightly controlled) and its interaction with additional proteins. These differences in location and trans-acting factor requirements account for the fact that PTB acts both as a suppressor of splicing and an activator of translation. In the latter case, the role of PTB in translation has been studied extensively and it appears that this protein is required for an alternative form of translation initiation that is mediated by a large RNA structural element termed an IRES (internal ribosome entry site) that allows the synthesis of picornaviral proteins and cellular proteins that function to control cell growth and cell death. In the present review, we discuss how PTB regulates these disparate processes.
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39
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Resnick M, Segall A, G GRK, Lupowitz Z, Zisapel N. Alternative splicing of neurexins: A role for neuronal polypyrimidine tract binding protein. Neurosci Lett 2008; 439:235-40. [DOI: 10.1016/j.neulet.2008.05.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Revised: 05/13/2008] [Accepted: 05/13/2008] [Indexed: 11/24/2022]
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40
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Repression of prespliceosome complex formation at two distinct steps by Fox-1/Fox-2 proteins. Mol Cell Biol 2008; 28:5507-16. [PMID: 18573872 DOI: 10.1128/mcb.00530-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Precise and robust regulation of alternative splicing provides cells with an essential means of gene expression control. However, the mechanisms that ensure the tight control of tissue-specific alternative splicing are not well understood. It has been demonstrated that robust regulation often results from the contributions of multiple factors to one particular splicing pathway. We report here a novel strategy used by a single splicing regulator that blocks the formation of two distinct prespliceosome complexes to achieve efficient regulation. Fox-1/Fox-2 proteins, potent regulators of alternative splicing in the heart, skeletal muscle, and brain, repress calcitonin-specific splicing of the calcitonin/CGRP pre-mRNA. Using biochemical analysis, we found that Fox-1/Fox-2 proteins block prespliceosome complex formation at two distinct steps through binding to two functionally important UGCAUG elements. First, Fox-1/Fox-2 proteins bind to the intronic site to inhibit SF1-dependent E' complex formation. Second, these proteins bind to the exonic site to block the transition of E' complex that escaped the control of the intronic site to E complex. These studies provide evidence for the first example of regulated E' complex formation. The two-step repression of presplicing complexes by a single regulator provides a powerful and accurate regulatory strategy.
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41
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Wang C, Norton JT, Ghosh S, Kim J, Fushimi K, Wu JY, Stack MS, Huang S. Polypyrimidine tract-binding protein (PTB) differentially affects malignancy in a cell line-dependent manner. J Biol Chem 2008; 283:20277-87. [PMID: 18499661 DOI: 10.1074/jbc.m803682200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA processing is altered during malignant transformation, and expression of the polypyrimidine tract-binding protein (PTB) is often increased in cancer cells. Although some data support that PTB promotes cancer, the functional contribution of PTB to the malignant phenotype remains to be clarified. Here we report that although PTB levels are generally increased in cancer cell lines from multiple origins and in endometrial adenocarcinoma tumors, there appears to be no correlation between PTB levels and disease severity or metastatic capacity. The three isoforms of PTB increase heterogeneously among different tumor cells. PTB knockdown in transformed cells by small interfering RNA decreases cellular growth in monolayer culture and to a greater extent in semi-solid media without inducing apoptosis. Down-regulation of PTB expression in a normal cell line reduces proliferation even more significantly. Reduction of PTB inhibits the invasive behavior of two cancer cell lines in Matrigel invasion assays but enhances the invasive behavior of another. At the molecular level, PTB in various cell lines differentially affects the alternative splicing pattern of the same substrates, such as caspase 2. Furthermore, overexpression of PTB does not enhance proliferation, anchorage-independent growth, or invasion in immortalized or normal cells. These data demonstrate that PTB is not oncogenic and can either promote or antagonize a malignant trait dependent upon the specific intra-cellular environment.
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Affiliation(s)
- Chen Wang
- Department of Cell and Molecular Biology, Feinberg School of Medicine of Northwestern University, Chicago, IL 60611, USA
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42
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Polypyrimidine tract binding protein induces human papillomavirus type 16 late gene expression by interfering with splicing inhibitory elements at the major late 5' splice site, SD3632. J Virol 2008; 82:3665-78. [PMID: 18216120 DOI: 10.1128/jvi.02140-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We have initiated a screen for cellular factors that can induce human papillomavirus type 16 (HPV-16) late gene expression in human cancer cells. We report that the overexpression of polypyrimidine tract binding protein (PTB), also known as heterologous nuclear ribonucleoprotein I (hnRNP I), induces HPV-16 late gene expression in cells transfected with subgenomic HPV-16 plasmids or with full-length HPV-16 genomes and in persistently HPV-16-infected cells. In contrast, other hnRNPs such as hnRNP B1/A2, hnRNP F, and hnRNP Q do not induce HPV-16 late gene expression. PTB activates SD3632, the only 5' splice site on the HPV-16 genome that is used exclusively by late mRNAs. PTB interferes with splicing inhibitory sequences located immediately upstream and downstream of SD3632, thereby activating late gene expression. One AU-rich PTB-responsive element was mapped to a 198-nucleotide sequence located downstream of SD3632. The deletion of this element induced HPV-16 late gene expression in the absence of PTB. Our results suggest that the overexpression of PTB interferes with cellular factors that interact with the inhibitory sequences. One may speculate that an increase in PTB levels or a reduction in the concentration of a PTB antagonist is required for the activation of HPV-16 late gene expression during the viral life cycle.
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Lahmann I, Fabienke M, Henneberg B, Pabst O, Vauti F, Minge D, Illenberger S, Jockusch BM, Korte M, Arnold HH. The hnRNP and cytoskeletal protein raver1 contributes to synaptic plasticity. Exp Cell Res 2007; 314:1048-60. [PMID: 18061163 DOI: 10.1016/j.yexcr.2007.10.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 10/26/2007] [Accepted: 10/31/2007] [Indexed: 12/18/2022]
Abstract
Raver1 is an hnRNP protein that interacts with the ubiquitous splicing regulator PTB and binds to cytoskeletal components like alpha-actinin and vinculin/metavinculin. Cell culture experiments suggested that raver1 functions as corepressor in PTB-regulated splicing reactions and may thereby increase proteome complexity. To determine the role of raver1 in vivo, we inactivated the gene by targeted disruption in the mouse. Here we report that raver1-deficient mice develop regularly to adulthood and show no obvious anatomical or behavioral defects. In keeping with this notion, cells from raver1-null mice were indistinguishable from wild type cells and displayed normal growth, motility, and cytoskeletal architecture in culture. Moreover, alternative splicing of exons, including the model exon 3 of alpha-tropomyosin, was not markedly changed in mutant mice, suggesting that the role of raver1 for PTB-mediated exon repression is not absolutely required to generate splice variants during mouse development. Interestingly however, loss of raver1 caused significantly reduced plasticity of synapses on acute hippocampal slices, as elicited by electrophysiological measurements of markedly lower LTP and LTD in mutant neurons. Our results provide evidence that raver1 may play an important role for the regulation of neuronal synaptic plasticity, possibly by controlling especially the late LTP via posttranscriptional mechanisms.
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Affiliation(s)
- Ines Lahmann
- Cell and Molecular Biology, Institute for Biochemistry and Biotechnology, Technical University of Braunschweig, Braunschweig, Germany
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44
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Marinescu V, Loomis PA, Ehmann S, Beales M, Potashkin JA. Regulation of retention of FosB intron 4 by PTB. PLoS One 2007; 2:e828. [PMID: 17786200 PMCID: PMC1952174 DOI: 10.1371/journal.pone.0000828] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 08/14/2007] [Indexed: 11/19/2022] Open
Abstract
One effect of stressors such as chronic drug administration is that sequence within the terminal exon of the transcription factor FosB is recognized as intronic and removed by alternative splicing. This results in an open-reading-frame shift that produces a translation stop codon and ultimately a truncated protein, termed DeltaFosB. In vitro splicing assays with control and mutated transcripts generated from a fosB mini-gene construct indicated a CU-rich sequence at the 3' end of intron 4 (I4) plays an important role in regulating fosB pre-mRNA splicing due to its binding of polypyrimidine tract binding protein (PTB). PTB binding to this sequence is dependent upon phosphorylation by protein kinase A and is blocked if the CU-rich sequence is mutated to a U-rich region. When this mutated fosB minigene is expressed in HeLa cells, the splicing efficiency of its product is increased compared to wild type. Moreover, transient transfection of PTB-1 in HeLa cells decreased the splicing efficiency of a wild type fosB minigene transcript. Depletion of PTB from nuclear extracts facilitated U2AF65 binding to wild type sequence in vitro, suggesting these proteins function in a dynamic equilibrium to modulate fosB pre-mRNA alternative splicing. These results demonstrate for the first time that phosphorylated PTB promotes intron retention and thereby silences the splicing of fosB I4.
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Affiliation(s)
- Victor Marinescu
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Patricia A. Loomis
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Svetlana Ehmann
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Mitchell Beales
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Judith A. Potashkin
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
- * To whom correspondence should be addressed. E-mail:
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Paradis C, Cloutier P, Shkreta L, Toutant J, Klarskov K, Chabot B. hnRNP I/PTB can antagonize the splicing repressor activity of SRp30c. RNA (NEW YORK, N.Y.) 2007; 13:1287-300. [PMID: 17548433 PMCID: PMC1924885 DOI: 10.1261/rna.403607] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The control of alternative pre-mRNA splicing often requires the participation of factors displaying synergistic or antagonistic activities. In the hnRNP A1 pre-mRNA, three elements promote the exclusion of alternative exon 7B, while a fourth intron element (CE9) represses splicing of exon 7B to the downstream exon. We have shown previously that the 5' portion of the 38-nucleotide-long CE9 element is bound by SRp30c, and that this interaction is important for repression in vitro. To determine whether SRp30c alone can impose repression, we tested a high-affinity SRp30c binding site that we identified using the SELEX protocol. We find that multiple high-affinity SRp30c sites are required to replicate the level of repression obtained with CE9, and that both the 5' and the 3' portions of CE9 contribute to SRp30c binding. Performing RNA affinity chromatography with the complete CE9 element recovered hnRNP I/PTB. Surprisingly however, His-tagged PTB reduced the binding of SRp30c to CE9 in a nuclear extract, stimulated splicing to a downstream 3' splice site, and relieved the CE9-mediated splicing repression in vitro. Our in vivo results are consistent with the notion that increasing PTB levels alleviates the repression imposed by CE9 to a downstream 3' splice site. Thus, PTB can function as an anti-repressor molecule to counteract the splicing inhibitory activity of SRp30c.
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Affiliation(s)
- Caroline Paradis
- RNA/RNP Group, Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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Alibhai IN, Green TA, Potashkin JA, Nestler EJ. Regulation of fosB and DeltafosB mRNA expression: in vivo and in vitro studies. Brain Res 2007; 1143:22-33. [PMID: 17324382 PMCID: PMC1880876 DOI: 10.1016/j.brainres.2007.01.069] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Revised: 01/03/2007] [Accepted: 01/15/2007] [Indexed: 12/11/2022]
Abstract
The transcription factor DeltaFosB, a truncated splice isoform of FosB, accumulates in brain after several types of chronic stimulation. This accumulation is thought to be mediated by the unique stability of DeltaFosB compared to all other Fos family proteins. The goal of the present study was to determine if the relative expression of the two fosB isoforms is also regulated at the mRNA level, thereby further contributing to the selective accumulation of DeltaFosB after chronic stimulation. First, unlike the protein, the half-life of DeltafosB mRNA is only slightly longer than that of full-length fosB mRNA both in cultured cells in vitro and in the brain in vivo. Additionally, similar to c-fos, both fosB isoforms are induced abundantly in striatum after acute administration of amphetamine or stress, and partially desensitize after chronic exposures. Surprisingly, the relative ratio of DeltafosB to fosB mRNA increases most significantly after acute, not chronic, stimulation. Finally, overexpression of polypyrimidine tract binding protein (PTB1), which regulates RNA splicing, in cultured cells decreases the relative expression of DeltafosB compared to fosB mRNA. Together, these findings suggest that splicing of fosB pre-mRNA is regulated by the quantity of unspliced transcript available to the splicing machinery. These data provide fundamental information concerning the generation of DeltafosB mRNA, and indicate that the selective accumulation of DeltaFosB protein with chronic stimulation does not involve its preferential generation by RNA splicing.
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Affiliation(s)
- Imran N Alibhai
- Department of Psychiatry and Center for Basic Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9070, USA
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Martinez-Contreras R, Cloutier P, Shkreta L, Fisette JF, Revil T, Chabot B. hnRNP proteins and splicing control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:123-47. [PMID: 18380344 DOI: 10.1007/978-0-387-77374-2_8] [Citation(s) in RCA: 273] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proteins of the heterogeneous nuclear ribonucleoparticles (hnRNP) family form a structurally diverse group of RNA binding proteins implicated in various functions in metazoans. Here we discuss recent advances supporting a role for these proteins in precursor-messenger RNA (pre-mRNA) splicing. Heterogeneous nuclear RNP proteins can repress splicing by directly antagonizing the recognition of splice sites, or can interfere with the binding of proteins bound to enhancers. Recently, hnRNP proteins have been shown to hinder communication between factors bound to different splice sites. Conversely, several reports have described a positive role for some hnRNP proteins in pre-mRNA splicing. Moreover, cooperative interactions between bound hnRNP proteins may encourage splicing between specific pairs of splice sites while simultaneously hampering other combinations. Thus, hnRNP proteins utilize a variety of strategies to control splice site selection in a manner that is important for both alternative and constitutive pre-mRNA splicing.
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48
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Lin S, Fu XD. SR proteins and related factors in alternative splicing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:107-22. [PMID: 18380343 DOI: 10.1007/978-0-387-77374-2_7] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
SR proteins are a family of RNA binding proteins that contain a signature RS domain enriched with serine/arginine repeats. The RS domain is also found in many other proteins, which are collectively referred to as SR-related proteins. Several prototypical SR proteins are essential splicing factors, but the majority of RS domain-containing factors are characterized by their ability to alter splice site selection in vitro or in transfected cells. SR proteins and SR-related proteins are generally believed to modulate splice site selection via RNA recognition motif-mediated binding to exonic splicing enhancers and RS domain-mediated protein-protein and protein-RNA interactions during spliceosome assembly. However, the biological function of individual RS domain-containing splicing regulators is complex because of redundant as well as competitive functions, context-dependent effects and regulation by cotranscriptional and post-translational events. This chapter will focus on our current mechanistic understanding of alternative splicing regulation by SR proteins and SR-related proteins and will discuss some of the questions that remain to be addressed in future research.
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Affiliation(s)
- Shengrong Lin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
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Dalziel M, Nunes NM, Furger A. Two G-rich regulatory elements located adjacent to and 440 nucleotides downstream of the core poly(A) site of the intronless melanocortin receptor 1 gene are critical for efficient 3' end processing. Mol Cell Biol 2006; 27:1568-80. [PMID: 17189425 PMCID: PMC1820467 DOI: 10.1128/mcb.01821-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cleavage and polyadenylation is an essential processing reaction required for the maturation of pre-mRNAs into stable, export- and translation-competent mature mRNA molecules. This reaction requires the assembly of a multimeric protein complex onto a bipartite core sequence element consisting of an AAUAAA hexamer and a GU/U-rich downstream sequence element. In this study we have analyzed 3' end processing of the human melanocortin 1 receptor gene (MC1R). The MC1R gene is an intron-free transcription unit, and its poly(A) site lacks a defined U/GU-rich element. We describe two G-rich sequence elements that are critical for efficient cleavage at the MC1R poly(A) site. The first element is located 30 nucleotides downstream of the cleavage site and acts as an essential closely positioned enhancer. The second G-rich region is positioned more than 440 nucleotides downstream of the MC1R processing site and is instrumental for optimal processing efficiency. Both G-rich sequences contain clusters of heterogeneous nuclear ribonucleoprotein binding motifs and act together to enhance cleavage at the MC1R poly(A) site.
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Affiliation(s)
- Martin Dalziel
- Genetics Unit, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
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50
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Zhu H, Zhou HL, Hasman RA, Lou H. Hu proteins regulate polyadenylation by blocking sites containing U-rich sequences. J Biol Chem 2006; 282:2203-10. [PMID: 17127772 DOI: 10.1074/jbc.m609349200] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A recent genome-wide bioinformatic analysis indicated that 54% of human genes undergo alternative polyadenylation. Although it is clear that differential selection of poly(A) sites can alter gene expression, resulting in significant biological consequences, the mechanisms that regulate polyadenylation are poorly understood. Here we report that the neuron-specific members of a family of RNA-binding proteins, Hu proteins, known to regulate mRNA stability and translation in the cytoplasm, play an important role in polyadenylation regulation. Hu proteins are homologs of the Drosophila embryonic lethal abnormal visual protein and contain three RNA recognition motifs. Using an in vitro polyadenylation assay with HeLa cell nuclear extract and recombinant Hu proteins, we have shown that Hu proteins selectively block both cleavage and poly(A) addition at sites containing U-rich sequences. Hu proteins have no effect on poly(A) sites that do not contain U-rich sequences or sites in which the U-rich sequences are mutated. All three RNA recognition motifs of Hu proteins are required for this activity. Overexpression of HuR in HeLa cells also blocks polyadenylation at a poly(A) signal that contains U-rich sequences. Hu proteins block the interaction between the polyadenylation cleavage stimulation factor 64-kDa subunit and RNA most likely through direct interaction with poly(A) cleavage stimulation factor 64-kDa subunit and cleavage and polyadenylation specificity factor 160-kDa subunit. These studies identify a novel group of mammalian polyadenylation regulators. Furthermore, they define a previously unknown nuclear function of Hu proteins.
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Affiliation(s)
- Hui Zhu
- Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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