1
|
Jobbins AM, Haberman N, Artigas N, Amourda C, Paterson HAB, Yu S, Blackford SJI, Montoya A, Dore M, Wang YF, Sardini A, Cebola I, Zuber J, Rashid ST, Lenhard B, Vernia S. Dysregulated RNA polyadenylation contributes to metabolic impairment in non-alcoholic fatty liver disease. Nucleic Acids Res 2022; 50:3379-3393. [PMID: 35293570 PMCID: PMC8989518 DOI: 10.1093/nar/gkac165] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
Pre-mRNA processing is an essential mechanism for the generation of mature mRNA and the regulation of gene expression in eukaryotic cells. While defects in pre-mRNA processing have been implicated in a number of diseases their involvement in metabolic pathologies is still unclear. Here, we show that both alternative splicing and alternative polyadenylation, two major steps in pre-mRNA processing, are significantly altered in non-alcoholic fatty liver disease (NAFLD). Moreover, we find that Serine and Arginine Rich Splicing Factor 10 (SRSF10) binding is enriched adjacent to consensus polyadenylation motifs and its expression is significantly decreased in NAFLD, suggesting a role mediating pre-mRNA dysregulation in this condition. Consistently, inactivation of SRSF10 in mouse and human hepatocytes in vitro, and in mouse liver in vivo, was found to dysregulate polyadenylation of key metabolic genes such as peroxisome proliferator-activated receptor alpha (PPARA) and exacerbate diet-induced metabolic dysfunction. Collectively our work implicates dysregulated pre-mRNA polyadenylation in obesity-induced liver disease and uncovers a novel role for SRSF10 in this process.
Collapse
Affiliation(s)
- Andrew M Jobbins
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Nejc Haberman
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Natalia Artigas
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Christopher Amourda
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Helen A B Paterson
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Sijia Yu
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Samuel J I Blackford
- Department of Metabolism, Digestion & Reproduction, Imperial College London, London W12 0NN, UK
| | - Alex Montoya
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Marian Dore
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alessandro Sardini
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion & Reproduction, Imperial College London, London W12 0NN, UK
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Sheikh Tamir Rashid
- Department of Metabolism, Digestion & Reproduction, Imperial College London, London W12 0NN, UK
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Santiago Vernia
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| |
Collapse
|
2
|
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: 28] [Impact Index Per Article: 9.3] [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.
Collapse
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
| |
Collapse
|
3
|
Shi J, Deng Y, Huang S, Huang C, Wang J, Xiang AP, Yao C. Suboptimal RNA-RNA interaction limits U1 snRNP inhibition of canonical mRNA 3' processing. RNA Biol 2019; 16:1448-1460. [PMID: 31242075 DOI: 10.1080/15476286.2019.1636596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
It is increasingly appreciated that U1 snRNP transcriptomically suppresses the usage of intronic polyadenylation site (PAS) of mRNAs, an outstanding question is why frequently used PASs are not suppressed. Here we found that U1 snRNP could be transiently associated with sequences upstream of actionable PASs in human cells, and RNA-RNA interaction might contribute to the association. By focusing on individual PAS, we showed that the stable assembly of U1 snRNP near PAS might be generally required for U1 inhibition of mRNA 3' processing. Therefore, actionable PASs that often lack optimal U1 snRNP docking site nearby is free from U1 inhibitory effect. Consistently, natural 5' splicing site (5'-SS) is moderately enriched ~250 nt upstream of intronic PASs whose usage is sensitive to functional knockdown of U1 snRNA. Collectively, our results provided an insight into how U1 snRNP selectively inhibits the usage of PASs in a cellular context, and supported a prevailing model that U1 snRNP scans pre-mRNA through RNA-RNA interaction to find a stable interaction site to exercise its function in pre-mRNA processing, including repressing the usage of cryptic PASs.
Collapse
Affiliation(s)
- Junjie Shi
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Yanhui Deng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Shanshan Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Chunliu Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Jinkai Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China.,RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University , Guangzhou , China.,Center for Precision Medicine, Sun Yat-sen University , Guangzhou , China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University , Guangzhou , China.,Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University , Guangzhou , China
| |
Collapse
|
4
|
Graham SV. Keratinocyte Differentiation-Dependent Human Papillomavirus Gene Regulation. Viruses 2017; 9:E245. [PMID: 28867768 PMCID: PMC5618011 DOI: 10.3390/v9090245] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 12/29/2022] Open
Abstract
Human papillomaviruses (HPVs) cause diseases ranging from benign warts to invasive cancers. HPVs infect epithelial cells and their replication cycle is tightly linked with the differentiation process of the infected keratinocyte. The normal replication cycle involves an early and a late phase. The early phase encompasses viral entry and initial genome replication, stimulation of cell division and inhibition of apoptosis in the infected cell. Late events in the HPV life cycle include viral genome amplification, virion formation, and release into the environment from the surface of the epithelium. The main proteins required at the late stage of infection for viral genome amplification include E1, E2, E4 and E5. The late proteins L1 and L2 are structural proteins that form the viral capsid. Regulation of these late events involves both cellular and viral proteins. The late viral mRNAs are expressed from a specific late promoter but final late mRNA levels in the infected cell are controlled by splicing, polyadenylation, nuclear export and RNA stability. Viral late protein expression is also controlled at the level of translation. This review will discuss current knowledge of how HPV late gene expression is regulated.
Collapse
Affiliation(s)
- Sheila V Graham
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK.
| |
Collapse
|
5
|
The Evolutionarily-conserved Polyadenosine RNA Binding Protein, Nab2, Cooperates with Splicing Machinery to Regulate the Fate of pre-mRNA. Mol Cell Biol 2016; 36:2697-2714. [PMID: 27528618 PMCID: PMC5064217 DOI: 10.1128/mcb.00402-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Numerous RNA binding proteins are deposited onto an mRNA transcript to modulate post-transcriptional processing events ensuring proper mRNA maturation. Defining the interplay between RNA binding proteins that couple mRNA biogenesis events is crucial for understanding how gene expression is regulated. To explore how RNA binding proteins control mRNA processing, we investigated a role for the evolutionarily conserved polyadenosine RNA binding protein, Nab2, in mRNA maturation within the nucleus. This work reveals that nab2 mutant cells accumulate intron-containing pre-mRNA in vivo We extend this analysis to identify genetic interactions between mutant alleles of nab2 and genes encoding the splicing factor, MUD2, and the RNA exosome, RRP6, with in vivo consequences of altered pre-mRNA splicing and poly(A) tail length control. As further evidence linking Nab2 proteins to splicing, an unbiased proteomic analysis of vertebrate Nab2, ZC3H14, identifies physical interactions with numerous components of the spliceosome. We validated the interaction between ZC3H14 and U2AF2/U2AF65 Taking all the findings into consideration, we present a model where Nab2/ZC3H14 interacts with spliceosome components to allow proper coupling of splicing with subsequent mRNA processing steps contributing to a kinetic proofreading step that allows properly processed mRNA to exit the nucleus and escape Rrp6-dependent degradation.
Collapse
|
6
|
Kaida D. The reciprocal regulation between splicing and 3'-end processing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:499-511. [PMID: 27019070 PMCID: PMC5071671 DOI: 10.1002/wrna.1348] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/05/2016] [Accepted: 02/22/2016] [Indexed: 12/14/2022]
Abstract
Most eukaryotic precursor mRNAs are subjected to RNA processing events, including 5′‐end capping, splicing and 3′‐end processing. These processing events were historically studied independently; however, since the early 1990s tremendous efforts by many research groups have revealed that these processing factors interact with each other to control each other's functions. U1 snRNP and its components negatively regulate polyadenylation of precursor mRNAs. Importantly, this function is necessary for protecting the integrity of the transcriptome and for regulating gene length and the direction of transcription. In addition, physical and functional interactions occur between splicing factors and 3′‐end processing factors across the last exon. These interactions activate or inhibit splicing and 3′‐end processing depending on the context. Therefore, splicing and 3′‐end processing are reciprocally regulated in many ways through the complex protein–protein interaction network. Although interesting questions remain, future studies will illuminate the molecular mechanisms underlying the reciprocal regulation. WIREs RNA 2016, 7:499–511. doi: 10.1002/wrna.1348 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Daisuke Kaida
- Frontier Research Core for Life Sciences, University of Toyama, Toyama, Japan
| |
Collapse
|
7
|
Zanzoni A, Marchese D, Agostini F, Bolognesi B, Cirillo D, Botta-Orfila M, Livi CM, Rodriguez-Mulero S, Tartaglia GG. Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein. Nucleic Acids Res 2013; 41:9987-98. [PMID: 24003031 PMCID: PMC3905859 DOI: 10.1093/nar/gkt794] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Previous evidence indicates that a number of proteins are able to interact with cognate mRNAs. These autogenous associations represent important regulatory mechanisms that control gene expression at the translational level. Using the catRAPID approach to predict the propensity of proteins to bind to RNA, we investigated the occurrence of autogenous associations in the human proteome. Our algorithm correctly identified binding sites in well-known cases such as thymidylate synthase, tumor suppressor P53, synaptotagmin-1, serine/ariginine-rich splicing factor 2, heat shock 70 kDa, ribonucleic particle-specific U1A and ribosomal protein S13. In addition, we found that several other proteins are able to bind to their own mRNAs. A large-scale analysis of biological pathways revealed that aggregation-prone and structurally disordered proteins have the highest propensity to interact with cognate RNAs. These findings are substantiated by experimental evidence on amyloidogenic proteins such as TAR DNA-binding protein 43 and fragile X mental retardation protein. Among the amyloidogenic proteins, we predicted that Parkinson’s disease-related α-synuclein is highly prone to interact with cognate transcripts, which suggests the existence of RNA-dependent factors in its function and dysfunction. Indeed, as aggregation is intrinsically concentration dependent, it is possible that autogenous interactions play a crucial role in controlling protein homeostasis.
Collapse
Affiliation(s)
- Andreas Zanzoni
- Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Bronzoni RVM, Madrid MCFS, Duarte DVB, Pellegrini VOA, Pacca CC, Carmo ACV, Zanelli CF, Valentini SR, Santacruz-Pérez C, Barbosa JARG, Lutz CS, Rahal P, Nogueira ML. The small nuclear ribonucleoprotein U1A interacts with NS5 from yellow fever virus. Arch Virol 2011; 156:931-8. [PMID: 21298455 DOI: 10.1007/s00705-011-0927-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 01/18/2011] [Indexed: 10/18/2022]
Abstract
The flavivirus NS5 protein is one of the most important proteins of the replication complex, and cellular proteins can interact with it. This study shows for the first time that the yellow fever virus (YFV) NS5 protein is able to interact with U1A, a protein involved in splicing and polyadenylation. We confirmed this interaction by GST-pulldown assay and by co-immunoprecipitation in YFV-infected cells. A region between amino acids 368 and 448 was identified as the site of interaction of the NS5 protein with U1A. This region was conserved among some flaviviruses of medical importance. The implications of this interaction for flavivirus replication are discussed.
Collapse
Affiliation(s)
- Roberta V M Bronzoni
- Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de Rio Preto, São José do Rio Preto 15090-000, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Martinson HG. An active role for splicing in 3′-end formation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:459-70. [DOI: 10.1002/wrna.68] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
10
|
Lutz CS, Moreira A. Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:22-31. [PMID: 21956967 DOI: 10.1002/wrna.47] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Alternative RNA processing mechanisms, including alternative splicing and alternative polyadenylation, are increasingly recognized as important regulators of gene expression. This article will focus on what has recently been described about alternative polyadenylation in development, differentiation, and disease in higher eukaryotes. We will also describe how the evolving global methodologies for examining the cellular transcriptome, both experimental and bioinformatic, are revealing new details about the complex nature of alternative 3(') end formation as well as interactions with other RNA-mediated and RNA processing mechanisms.
Collapse
Affiliation(s)
- Carol S Lutz
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, NJ, USA.
| | | |
Collapse
|
11
|
Newnham CM, Hall-Pogar T, Liang S, Wu J, Tian B, Hu J, Lutz CS. Alternative polyadenylation of MeCP2: Influence of cis-acting elements and trans-acting factors. RNA Biol 2010; 7:361-72. [PMID: 20400852 DOI: 10.4161/rna.7.3.11564] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The human MeCP2 gene encodes a ubiquitously expressed methyl CpG binding protein. Mutations in this gene cause a neurodevelopmental disorder called Rett Syndrome (RS). Mutations identified in the coding region of MeCP2 account for approximately 65% of all RS cases. However, 35% of all patients do not show mutations in the coding region of MeCP2, suggesting that mutations in non-coding regions likely exist that affect MeCP2 expression rather than protein function. The gene is unusual in that is has a >8.5 kb 3' untranslated region (3' UTR), and the size of the 3'UTR is differentially regulated in various tissues because of distinct polyadenylation signals. We have identified putative cis-acting auxiliary regulatory elements that play a role in alternative polyadenylation of MeCP2 using an in vivo polyadenylation reporter assay and in a luciferase assay. These cis-acting auxiliary elements are found both upstream and downstream of the core CPSF binding sites. Mutation of one of these cis-acting auxiliary elements, a G-rich element (GRS) significantly reduced MeCP2 polyadenylation efficiency in vivo. We further investigated what trans-acting factor(s) might be binding to this cis-acting element and found that hnRNP F protein binds specifically to the element. We next investigated the MeCP2 3' UTRs by performing quantitative real-time PCR; the data suggest that altered RNA stability is not a major factor in differential MeCP2 3' UTR usage. In sum, the mechanism(s) of regulated alternative 3'UTR usage of MeCP2 are complex, and insight into these mechanisms will aid our understanding of the factors that influence MeCP2 expression.
Collapse
Affiliation(s)
- Catherine M Newnham
- Department of Physiology and Experimental Medicine, University of Toronto, Toronto, ON, Canada
| | | | | | | | | | | | | |
Collapse
|
12
|
Neilson JR, Sandberg R. Heterogeneity in mammalian RNA 3' end formation. Exp Cell Res 2010; 316:1357-64. [PMID: 20211174 DOI: 10.1016/j.yexcr.2010.02.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 02/28/2010] [Indexed: 11/19/2022]
Abstract
Precisely directed cleavage and polyadenylation of mRNA is a fundamental part of eukaryotic gene expression. Yet, 3' end heterogeneity has been documented for thousands of mammalian genes, and usage of one cleavage and polyadenylation signal over another has been shown to impact gene expression in many cases. Building upon the rich biochemical and genetic understanding of the 3' end formation, recent genomic studies have begun to suggest that widespread changes in mRNA cleavage and polyadenylation may be a part of large, dynamic gene regulatory programs. In this review, we begin with a modest overview of the studies that defined the mechanisms of mammalian 3' end formation, and then discuss how recent genomic studies intersect with these more traditional approaches, showing that both will be crucial for expanding our understanding of this facet of gene regulation.
Collapse
Affiliation(s)
- Joel R Neilson
- Department of Molecular Physiology and Biophysics and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | |
Collapse
|
13
|
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: 296] [Impact Index Per Article: 19.7] [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.
Collapse
Affiliation(s)
- Stefania Millevoi
- Institut National de la Santé et de la Recherche Médicale U563, Toulouse, F-31000, France.
| | | |
Collapse
|
14
|
Maciolek NL, McNally MT. Characterization of Rous sarcoma virus polyadenylation site use in vitro. Virology 2008; 374:468-76. [PMID: 18272196 PMCID: PMC2413101 DOI: 10.1016/j.virol.2008.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 12/13/2007] [Accepted: 01/10/2008] [Indexed: 11/22/2022]
Abstract
Polyadenylation of Rous sarcoma virus (RSV) RNA is inefficient, as approximately 15% of RSV RNAs represent read-through transcripts that use a downstream cellular polyadenylation site (poly(A) site). Read-through transcription has implications for the virus and the host since it is associated with oncogene capture and tumor induction. To explore the basis of inefficient RSV RNA 3'-end formation, we characterized RSV polyadenylation in vitro using HeLa cell nuclear extracts and HEK293 whole cell extracts. RSV polyadenylation substrates composed of the natural 3' end of viral RNA and various lengths of upstream sequence showed little or no polyadenylation, indicating that the RSV poly(A) site is suboptimal. Efficiently used poly(A) sites often have identifiable upstream and downstream elements (USEs and DSEs) in close proximity to the conserved AAUAAA signal. The sequences upstream and downstream of the RSV poly(A) site deviate from those found in efficiently used poly(A) sites, which may explain inefficient RSV polyadenylation. To assess the quality of the RSV USEs and DSEs, the well-characterized SV40 late USEs and/or DSEs were substituted for the RSV elements and vice versa, which showed that the USEs and DSEs from RSV are suboptimal but functional. CstF interacted poorly with the RSV polyadenylation substrate, and the inactivity of the RSV poly(A) site was at least in part due to poor CstF binding since tethering CstF to the RSV substrate activated polyadenylation. Our data are consistent with poor polyadenylation factor binding sites in both the USE and DSE as the basis for inefficient use of the RSV poly(A) site and point to the importance of additional elements within RSV RNA in promoting 3' end formation.
Collapse
Affiliation(s)
- Nicole L. Maciolek
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, 8701, Watertown Plank Road, Milwaukee, WI 53226 USA
| | - Mark T. McNally
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, 8701, Watertown Plank Road, Milwaukee, WI 53226 USA
| |
Collapse
|
15
|
Jagus R, Beckler GS. Overview of eukaryotic in vitro translation and expression systems. ACTA ACUST UNITED AC 2008; Chapter 11:Unit 11.1. [PMID: 18228417 DOI: 10.1002/0471143030.cb1101s00] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The ability to investigate cellular processes in vitro permits detailed analysis of the process and its molecular components. Eukaryotic translation and expression is one system that has been well studied. This overview describes the development of in vitro systems, including such approaches as continuous-flow systems, coupled transcription/translation, and the incorporation of non-natural amino acids. It also discusses molecular and genetic studies to probe translation, including post-translational fate of the synthesized proteins.
Collapse
Affiliation(s)
- Rosemary Jagus
- Center of Marine and Biotechnology and Greenebaum Cancer Center, Baltimore, Maryland, USA
| | | |
Collapse
|
16
|
Friend K, Lovejoy AF, Steitz JA. U2 snRNP binds intronless histone pre-mRNAs to facilitate U7-snRNP-dependent 3' end formation. Mol Cell 2008; 28:240-52. [PMID: 17964263 PMCID: PMC2149891 DOI: 10.1016/j.molcel.2007.09.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 08/08/2007] [Accepted: 09/14/2007] [Indexed: 11/17/2022]
Abstract
In metazoa, pre-mRNA 3' end formation occurs via two pathways: cleavage/polyadenylation for the majority of RNA polymerase II transcripts and U7-snRNP-dependent cleavage for replication-dependent histone pre-mRNAs. An RNA element derived from a replication-dependent histone gene affects multiple steps of pre-mRNA processing. Here, we demonstrate that a portion of this RNA element, present in the majority of histone mRNAs, stimulates U7-snRNP-dependent cleavage. Surprisingly, this element binds U2 snRNP, although it is derived from an intronless mRNA. Specifically, SF3b, a U2 and U12-snRNP component, contacts the RNA element both in vitro and in vivo in conjunction with hPrp43, a DEAH-box helicase. Tethering either U2 or U12 snRNP to histone pre-mRNA substrates stimulates U7-snRNP-dependent cleavage in vitro and in vivo. Finally, we show that U2 snRNP associates with histone pre-mRNAs in vivo. We conclude that U2 snRNP plays a nonsplicing role in histone mRNA maturation.
Collapse
Affiliation(s)
- Kyle Friend
- Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | | | | |
Collapse
|
17
|
Hall-Pogar T, Liang S, Hague LK, Lutz CS. Specific trans-acting proteins interact with auxiliary RNA polyadenylation elements in the COX-2 3'-UTR. RNA (NEW YORK, N.Y.) 2007; 13:1103-15. [PMID: 17507659 PMCID: PMC1894925 DOI: 10.1261/rna.577707] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Two cyclooxygenase (COX) enzymes, COX-1 and COX-2, are present in human cells. While COX-1 is constitutively expressed, COX-2 is inducible and up-regulated in response to many signals. Since increased transcriptional activity accounts for only part of COX-2 up-regulation, we chose to explore other RNA processing mechanisms in the regulation of this gene. Previously, we showed that COX-2 is regulated by alternative polyadenylation, and that the COX-2 proximal polyadenylation signal contains auxiliary upstream sequence elements (USEs) that are very important in efficient polyadenylation. To explore trans-acting protein factors interacting with these cis-acting RNA elements, we performed pull-down assays with HeLa nuclear extract and biotinylated RNA oligonucleotides representing COX-2 USEs. We identified PSF, p54(nrb), PTB, and U1A as proteins specifically bound to the COX-2 USEs. We further explored their participation in polyadenylation using MS2 phage coat protein-MS2 RNA binding site tethering assays, and found that tethering any of these four proteins to the COX-2 USE mutant RNA can compensate for these cis-acting elements. Finally, we suggest that these proteins (p54(nrb), PTB, PSF, and U1A) may interact as a complex since immunoprecipitations of the transfected MS2 fusion proteins coprecipitate the other proteins.
Collapse
Affiliation(s)
- Tyra Hall-Pogar
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA
| | | | | | | |
Collapse
|
18
|
Qiu J, Cheng F, Pintel D. Distance-dependent processing of adeno-associated virus type 5 RNA is controlled by 5' exon definition. J Virol 2007; 81:7974-84. [PMID: 17507471 PMCID: PMC1951275 DOI: 10.1128/jvi.00714-07] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adeno-associated virus type 5 (AAV5) is unique among human AAV serotypes in that it uses a polyadenylation site [(pA)p] within the single small intron in the center of the genome. We previously reported that inhibition of polyadenylation at (pA)p, necessary for read-through of P41-generated capsid gene pre-mRNAs which are subsequently spliced, requires binding of U1 snRNP to the upstream donor. Inhibition was reduced as the distance between the cap site and the donor was increased (increasing the size of the 5' exon). Here, we have demonstrated that U1-70K is a key component of U1 snRNP that mediates inhibition of polyadenylation at (pA)p. Furthermore, introduction of a U-rich stretch, predicted to target TIA-1 and thus increase the affinity of U1 snRNP binding to the intervening donor site, significantly augmented inhibition of (pA)p, while depletion of TIA-1 by siRNA increased (pA)p read-through. Finally, artificially tethering the cap binding complex (CBC) components CBP80 and CBP20 upstream of the intron donor increased inhibition of polyadenylation at (pA)p. Our results suggest that interaction with the CBC strengthens U1 snRNP binding to the downstream intron donor in a manner inversely proportional to the size of the 5' exon, thus governing the competition between intron splicing and polyadenylation at (pA)p. This competition must be optimized to program both the levels of polyadenylation of P7- and P19-generated RNA at (pA)p required to produce proper levels of the essential Rep proteins and the splicing of P41-generated RNAs to produce the proper ratio of capsid proteins during AAV5 infection.
Collapse
Affiliation(s)
- Jianming Qiu
- Department of Molecular Microbiology and Immunology, University of Missouri--Columbia, School of Medicine, Life Sciences Center, Columbia, Missouri 65212, USA
| | | | | |
Collapse
|
19
|
Schambach A, Galla M, Maetzig T, Loew R, Baum C. Improving transcriptional termination of self-inactivating gamma-retroviral and lentiviral vectors. Mol Ther 2007; 15:1167-73. [PMID: 17406345 DOI: 10.1038/sj.mt.6300152] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Adverse events relating to insertional mutagenesis have reinforced the interest in self-inactivating (SIN) gamma-retroviral and lentiviral vectors without enhancer-promoter sequences in the U3 region of the long terminal repeats. However, SIN vectors suffer from leaky transcriptional termination, increasing the probability of read-through into cellular genes. To improve 3' end processing, we incorporated seven upstream polyadenylation enhancer elements (or upstream sequence elements, USEs) derived from viral or cellular genes into the 3' U3 region of gamma-retroviral and lentiviral SIN vectors. A 100-base-pair sequence representing a recombinant direct repeat of the USE derived from simian virus 40 (2xSV USE) gave the best results, improving both titer and gene expression. In both gamma-retroviral and lentiviral SIN vectors, the 2xSV USE partially substituted for effects provided by the much larger post-transcriptional regulatory element derived from woodchuck hepatitis virus (wPRE). By northern blot and reporter assays, we found that the 2xSV USE greatly improved proper messenger RNA (mRNA) processing at the retroviral termination signal. Importantly, the 2xSV USE was superior to the wPRE in suppressing transcriptional read-through, improving not only vector efficiency but potentially also biosafety.
Collapse
Affiliation(s)
- Axel Schambach
- 1Department of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | | | | | | |
Collapse
|
20
|
Monarez RR, MacDonald CC, Dass B. Polyadenylation proteins CstF-64 and tauCstF-64 exhibit differential binding affinities for RNA polymers. Biochem J 2007; 401:651-8. [PMID: 17029590 PMCID: PMC1770853 DOI: 10.1042/bj20061097] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
CstF-64 (cleavage stimulation factor-64), a major regulatory protein of polyadenylation, is absent during male meiosis. Therefore a paralogous variant, tauCstF-64 is expressed in male germ cells to maintain normal spermatogenesis. Based on sequence differences between tauCstF-64 and CstF-64, and on the high incidence of alternative polyadenylation in testes, we hypothesized that the RBDs (RNA-binding domains) of tauCstF-64 and CstF-64 have different affinities for RNA elements. We quantified K(d) values of CstF-64 and tauCstF-64 RBDs for various ribopolymers using an RNA cross-linking assay. The two RBDs had similar affinities for poly(G)18, poly(A)18 or poly(C)18, with affinity for poly(C)18 being the lowest. However, CstF-64 had a higher affinity for poly(U)18 than tauCstF-64, whereas it had a lower affinity for poly(GU)9. Changing Pro-41 to a serine residue in the CstF-64 RBD did not affect its affinity for poly(U)18, but changes in amino acids downstream of the C-terminal alpha-helical region decreased affinity towards poly(U)18. Thus we show that the two CstF-64 paralogues differ in their affinities for specific RNA sequences, and that the region C-terminal to the RBD is mportant in RNA sequence recognition. This supports the hypothesis that tauCstF-64 promotes germ-cell-specific patterns of polyadenylation by binding to different downstream sequence elements.
Collapse
Affiliation(s)
- Roberto R Monarez
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
| | | | | |
Collapse
|
21
|
Charron M, Chern JY, Wright WW. The cathepsin L first intron stimulates gene expression in rat sertoli cells. Biol Reprod 2007; 76:813-24. [PMID: 17229931 DOI: 10.1095/biolreprod.106.057851] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Large amounts of cathepsin L (CTSL), a cysteine protease required for quantitatively normal spermatogenesis, are synthesized by mouse and rat Sertoli cells during stages VI to VII of the cycle of the seminiferous epithelium. We previously demonstrated that all of the regulatory elements required in vivo for both Sertoli cell- and stage-specific expression of the Ctsl gene are present within a ~3-kb genomic fragment that contains 2065 nucleotides upstream of the transcription start site and 977 nucleotides of downstream sequence. Most of the downstream region encodes the first intron. In this study, transient transfection assays using primary Sertoli cell cultures and the TM4 Sertoli cell line established that the Ctsl first intron increased reporter gene activity by ~5-fold. While the intron-mediated enhancement in reporter gene activity was not restricted to the Ctsl promoter, positioning the first intron upstream of the Ctsl promoter in either orientation abolished its stimulatory activity, suggesting that it does not contain a typical enhancer. Mutating the 5'-splice site of the Ctsl first intron or replacing the first intron by the Ctsl fourth intron abolished the stimulatory effect. Finally, the intron-dependent increase in reporter gene activity could be explained in part by an increase in the amounts of total RNA and transcript polyadenylation. Results from this study suggest that the stimulatory effect mediated by the Ctsl first intron may explain in part why Sertoli cells in seminiferous tubules at stages VI to VII produce high levels of CTSL.
Collapse
Affiliation(s)
- Martin Charron
- Division of Reproductive Biology, Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland 21205, USA.
| | | | | |
Collapse
|
22
|
Németh ZH, Lutz CS, Csóka B, Deitch EA, Leibovich SJ, Gause WC, Tone M, Pacher P, Vizi ES, Haskó G. Adenosine augments IL-10 production by macrophages through an A2B receptor-mediated posttranscriptional mechanism. THE JOURNAL OF IMMUNOLOGY 2006; 175:8260-70. [PMID: 16339566 PMCID: PMC2000336 DOI: 10.4049/jimmunol.175.12.8260] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Adenosine receptor ligands have anti-inflammatory effects and modulate immune responses by up-regulating IL-10 production by immunostimulated macrophages. The adenosine receptor family comprises G protein-coupled heptahelical transmembrane receptors classified into four types: A1, A2A, A2B, and A3. Our understanding of the signaling mechanisms leading to enhanced IL-10 production following adenosine receptor occupancy on macrophages is limited. In this study, we demonstrate that adenosine receptor occupancy increases IL-10 production by LPS-stimulated macrophages without affecting IL-10 promoter activity and IL-10 mRNA levels, indicating a posttranscriptional mechanism. Transfection experiments with reporter constructs containing sequences corresponding to the AU-rich 3'-untranslated region (UTR) of IL-10 mRNA confirmed that adenosine receptor activation acts by relieving the translational repressive effect of the IL-10 3'-UTR. By contrast, adenosine receptor activation failed to liberate the translational arrest conferred by the 3'-UTR of TNF-alpha mRNA. The IL-10 3'-UTR formed specific complexes with proteins present in cytoplasmic extracts of RAW 264.7 cells. Adenosine enhanced binding of proteins to a region of the IL-10 3'-UTR containing the GUAUUUAUU nonamer. The stimulatory effect of adenosine on IL-10 production was mediated through the A(2B) receptor, because the order of potency of selective agonists was 5'-N-ethylcarboxamidoadenosine (NECA) > N6-(3-iodobenzyl)-adenosine-5'-N-methyluronamide (IB-MECA) > 2-chloro-N6-cyclopentyladenosine (CCPA) = 2-p-(2-carboxyethyl)phenethylamino-5'-N-ethyl-carboxamidoadenosine (CGS-21680). Also, the selective A2B antagonist, alloxazine, prevented the effect of adenosine. Collectively, these studies identify a novel pathway in which activation of a G protein-coupled receptor augments translation of an anti-inflammatory gene.
Collapse
Affiliation(s)
- Zoltán H. Németh
- Department of Surgery, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, Newark, NJ 07103
| | - Carol S. Lutz
- Departments of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, Newark, NJ 07103
| | - Balázs Csóka
- Department of Surgery, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, Newark, NJ 07103
| | - Edwin A. Deitch
- Department of Surgery, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, Newark, NJ 07103
| | - S. Joseph Leibovich
- Departments of Cell Biology and Molecular Medicine, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, Newark, NJ 07103
| | - William C. Gause
- Department of Medicine, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, Newark, NJ 07103
| | - Masahide Tone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Pál Pacher
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20892
| | - E. Sylvester Vizi
- Department of Pharmacology, Institute of Experimental Medicine, Budapest, Hungary
| | - György Haskó
- Department of Surgery, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, Newark, NJ 07103
- Address correspondence and reprint requests to Dr. György Haskó, Department of Surgery, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, University Heights, Newark, NJ 07103. E-mail address:
| |
Collapse
|
23
|
Fritz DT, Jiang S, Xu J, Rogers MB. A polymorphism in a conserved posttranscriptional regulatory motif alters bone morphogenetic protein 2 (BMP2) RNA:protein interactions. Mol Endocrinol 2006; 20:1574-86. [PMID: 16497730 DOI: 10.1210/me.2005-0469] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The bone morphogenetic protein (BMP)2 gene has been genetically linked to osteoporosis and osteoarthritis. We have shown that the 3'-untranslated regions (UTR) of BMP2 genes from mammals to fishes are extraordinarily conserved. This indicates that the BMP2 3'-UTR is under stringent selective pressure. We present evidence that the conserved region is a strong posttranscriptional regulator of BMP2 expression. Polymorphisms in cis-regulatory elements have been proven to influence susceptibility to a growing number of diseases. A common single nucleotide polymorphism (SNP) disrupts a putative posttranscriptional regulatory motif, an AU-rich element, within the BMP2 3'-UTR. The affinity of specific proteins for the rs15705 SNP sequence differs from their affinity for the normal human sequence. More importantly, the in vitro decay rate of RNAs with the SNP is higher than that of RNAs with the normal sequence. Such changes in mRNA:protein interactions may influence the posttranscriptional mechanisms that control BMP2 gene expression. The consequent alterations in BMP2 protein levels may influence the development or physiology of bone or other BMP2-influenced tissues.
Collapse
Affiliation(s)
- David T Fritz
- Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey-New Jersey Medical School, Newark, New Jersey 07101-1709, USA
| | | | | | | |
Collapse
|
24
|
Rigo F, Kazerouninia A, Nag A, Martinson HG. The RNA tether from the poly(A) signal to the polymerase mediates coupling of transcription to cleavage and polyadenylation. Mol Cell 2006; 20:733-45. [PMID: 16337597 DOI: 10.1016/j.molcel.2005.09.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Revised: 09/15/2005] [Accepted: 09/30/2005] [Indexed: 11/15/2022]
Abstract
We have investigated the mechanism by which transcription accelerates cleavage and polyadenylation in vitro. By using a coupled transcription-processing system, we show that rapid and efficient 3' end processing occurs in the absence of crowding agents like polyvinyl alcohol. The continuity of the RNA from the poly(A) signal down to the polymerase is critical to this processing. If this tether is cut with DNA oligonucleotides and RNaseH during transcription, the efficiency of processing is drastically reduced. The polymerase is known to be an integral part of the cleavage and polyadenylation apparatus. RNA polymerase II pull-down and immobilized template experiments suggest that the role of the tether is to hold the poly(A) signal close to the polymerase during the early stages of processing complex assembly until the complex is sufficiently mature to remain stably associated with the polymerase on its own.
Collapse
Affiliation(s)
- Frank Rigo
- Department of Chemistry and Biochemistry and The Molecular Biology Institute, University of California, Los Angeles, 90095, USA
| | | | | | | |
Collapse
|
25
|
Liang S, Lutz CS. p54nrb is a component of the snRNP-free U1A (SF-A) complex that promotes pre-mRNA cleavage during polyadenylation. RNA (NEW YORK, N.Y.) 2006; 12:111-21. [PMID: 16373496 PMCID: PMC1370891 DOI: 10.1261/rna.2213506] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Accepted: 10/12/2005] [Indexed: 05/05/2023]
Abstract
The U1 snRNP-A (U1A) protein has been known for many years as a component of the U1 snRNP. We have previously described a form of U1A present in human cells in significant amounts that is not associated with the U1 snRNP or U1 RNA but instead is part of a novel complex of non-snRNP proteins that we have termed snRNP-free U1A, or SF-A. Antibodies that specifically recognize this complex inhibit in vitro splicing and polyadenylation of pre-mRNA, suggesting that this complex may play an important functional role in these mRNA-processing activities. This finding was underscored by the determination that one of the components of this complex is the polypyrimidine-tract-binding protein-associated splicing factor, PSF. In order to further our studies on this complex and to determine the rest of the components of the SF-A complex, we prepared several stable HeLa cell lines that overexpress a tandem-affinity-purification-tagged version of U1A (TAP-tagged U1A). Nuclear extract was prepared from one of these cell lines, line 107, and affinity purification was performed along with RNase treatment. We have used mass spectrometry analysis to identify the candidate factors that associate with U1A. We have now identified and characterized PSF, p54(nrb), and p68 as novel components of the SF-A complex. We have explored the function of this complex in RNA processing, specifically cleavage and polyadenylation, by performing immunodepletions followed by reconstitution experiments, and have found that p54(nrb) is critical.
Collapse
Affiliation(s)
- Songchun Liang
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School MSB E671, 185 S. Orange Avenue, Newark, NJ 07103, USA
| | | |
Collapse
|
26
|
Zhang H, Lee JY, Tian B. Biased alternative polyadenylation in human tissues. Genome Biol 2005; 6:R100. [PMID: 16356263 PMCID: PMC1414089 DOI: 10.1186/gb-2005-6-12-r100] [Citation(s) in RCA: 235] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 08/31/2005] [Accepted: 10/18/2005] [Indexed: 11/15/2022] Open
Abstract
Bioinformatic analyses of the occurrence and mechanism of alternative polyadenylation in different human tissues reveals systematic differences among tissues and suggests the involvement of both trans- and cis-regulatory elements. Background Alternative polyadenylation is one of the mechanisms in human cells that give rise to a variety of transcripts from a single gene. More than half of the human genes have multiple polyadenylation sites (poly(A) sites), leading to variable mRNA and protein products. Previous studies of individual genes have indicated that alternative polyadenylation could occur in a tissue-specific manner. Results We set out to systematically investigate the occurrence and mechanism of alternative polyadenylation in different human tissues using bioinformatic approaches. Using expressed sequence tag (EST) data, we investigated 42 distinct tissue types. We found that several tissues tend to use poly(A) sites that are biased toward certain locations of a gene, such as sites located in introns or internal exons, and various sites in the exon located closest to the 3' end. We also identified several tissues, including eye, retina and placenta, that tend to use poly(A) sites not frequently used in other tissues. By exploring microarray expression data, we analyzed over 20 genes whose protein products are involved in the process or regulation of mRNA polyadenylation. Several brain tissues showed high concordance of gene expression of these genes with each other, but low concordance with other tissue types. By comparing genomic regions surrounding poly(A) sites preferentially used in brain tissues with those in other tissues, we identified several cis-regulatory elements that were significantly associated with brain-specific poly(A) sites. Conclusion Our results indicate that there are systematic differences in poly(A) site usage among human tissues, and both trans-acting factors and cis-regulatory elements may be involved in regulating alternative polyadenylation in different tissues.
Collapse
Affiliation(s)
- Haibo Zhang
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Ju Youn Lee
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Bin Tian
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| |
Collapse
|
27
|
Forbes KP, Addepalli B, Hunt AG. An Arabidopsis Fip1 homolog interacts with RNA and provides conceptual links with a number of other polyadenylation factor subunits. J Biol Chem 2005; 281:176-86. [PMID: 16282318 DOI: 10.1074/jbc.m510964200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protein Fip1 is an important subunit of the eukaryotic polyadenylation apparatus, since it provides a bridge of sorts between poly(A) polymerase, other subunits of the polyadenylation apparatus, and the substrate RNA. In this study, a previously unreported Arabidopsis Fip1 homolog is characterized. The gene for this protein resides on chromosome V and encodes a 1196-amino acid polypeptide. Yeast two-hybrid and in vitro assays indicate that the N-terminal 137 amino acids of the Arabidopsis Fip1 protein interact with poly(A) polymerase (PAP). This domain also stimulates the activity of the PAP. Interestingly, this part of the Arabidopsis Fip1 interacts with Arabidopsis homologs of CstF77, CPSF30, CFIm-25, and PabN1. The interactions with CstF77, CPSF30, and CFIm-25 are reminiscent in various respects of similar interactions seen in yeast and mammals, although the part of the Arabidopsis Fip1 protein that participates in these interactions has no apparent counterpart in other eukaryotic Fip1 proteins. Interactions between Fip1 and PabN1 have not been reported in other systems; this may represent plant-specific associations. The C-terminal 789 amino acids of the Arabidopsis Fip1 protein were found to contain an RNA-binding domain; this domain correlated with an intact arginine-rich region and had a marked preference for poly(G) among the four homopolymers studied. These results indicate that the Arabidopsis Fip1, like its human counterpart, is an RNA-binding protein. Moreover, they provide conceptual links between PAP and several other Arabidopsis polyadenylation factor subunit homologs.
Collapse
Affiliation(s)
- Kevin P Forbes
- Plant Physiology, Biochemistry, and Molecular Biology Program, Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312, USA
| | | | | |
Collapse
|
28
|
Sutherland LC, Rintala-Maki ND, White RD, Morin CD. RNA binding motif (RBM) proteins: a novel family of apoptosis modulators? J Cell Biochem 2005; 94:5-24. [PMID: 15514923 DOI: 10.1002/jcb.20204] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RBM5 is a known modulator of apoptosis, an RNA binding protein, and a putative tumor suppressor. Originally identified as LUCA-15, and subsequently as H37, it was designated "RBM" (for RNA Binding Motif) due to the presence of two RRM (RNA Recognition Motif) domains within the protein coding sequence. Recently, a number of proteins have been attributed with this same RBM designation, based on the presence of one or more RRM consensus sequences. One such protein, RBM3, was also recently found to have apoptotic modulatory capabilities. The high sequence homology at the amino acid level between RBM5, RBM6, and particularly, RBM10 suggests that they, too, may play an important role in regulating apoptosis. It is the intent of this article to ammalgamate the data on the ten originally identified RBM proteins in order to question the existence of a novel family of RNA binding apoptosis regulators.
Collapse
Affiliation(s)
- Leslie C Sutherland
- Tumour Biology Group, Northeastern Ontario Regional Cancer Centre, 41 Ramsey Lake Road, Sudbury, Ontario P3E 5J1, Canada.
| | | | | | | |
Collapse
|
29
|
Abstract
A biologically important human gene, cyclooxygenase-2 (COX-2), has been proposed to be regulated at many levels. While COX-1 is constitutively expressed in cells, COX-2 is inducible and is upregulated in response to many signals. Since increased transcriptional activity accounts for only part of the upregulation of COX-2, we chose to explore other RNA processing mechanisms in the regulation of this gene. We performed a comprehensive bioinformatics survey, the first of its kind known for human COX-2, which revealed that the human COX-2 gene has alternative polyadenylation (proximal and distal sites) and suggested that use of the alternative polyadenylation signals has tissue specificity. We experimentally established this in HepG2 and HT29 cells. We used an in vivo polyadenylation assay to examine the relative strength of the COX-2 proximal and distal polyadenylation signals, and have shown that the proximal polyadenylation signal is much weaker than the distal one. The efficiency of utilization of many suboptimal mammalian polyadenylation signals is affected by sequence elements located upstream of the AAUAAA, known as upstream efficiency elements (USEs). Here, we used in vivo polyadenylation assays in multiple cell lines to demonstrate that the COX-2 proximal polyadenylation signal contains USEs, mutation of the USEs substantially decreased usage of the proximal signal, and that USE spacing relative to the polyadenylation signal was significant. In addition, mutation of the COX-2 proximal polyadenylation signal to a more optimal sequence enhanced polyadenylation efficiency 3.5-fold. Our data suggest for the first time that alternative polyadenylation of COX-2 is an important post-transcriptional regulatory event.
Collapse
Affiliation(s)
- Tyra Hall-Pogar
- Department of Biochemistry and Molecular Biology, UMDNJ–New Jersey Medical SchoolNewark, NJ 07101, USA
- Graduate School of Biomedical Sciences, UMDNJ–New Jersey Medical SchoolNewark, NJ 07101, USA
| | - Haibo Zhang
- Department of Biochemistry and Molecular Biology, UMDNJ–New Jersey Medical SchoolNewark, NJ 07101, USA
- Bioinformatics Center, UMDNJ–New Jersey Medical SchoolNewark, NJ 07101, USA
| | - Bin Tian
- Department of Biochemistry and Molecular Biology, UMDNJ–New Jersey Medical SchoolNewark, NJ 07101, USA
- Graduate School of Biomedical Sciences, UMDNJ–New Jersey Medical SchoolNewark, NJ 07101, USA
- Bioinformatics Center, UMDNJ–New Jersey Medical SchoolNewark, NJ 07101, USA
| | - Carol S. Lutz
- Department of Biochemistry and Molecular Biology, UMDNJ–New Jersey Medical SchoolNewark, NJ 07101, USA
- Graduate School of Biomedical Sciences, UMDNJ–New Jersey Medical SchoolNewark, NJ 07101, USA
- To whom correspondence should be addressed at Department of Biochemistry and Molecular Biology, UMDNJ–New Jersey Medical School, MSB E671, 185 South Orange Avenue, Newark, NJ 07101, USA. Tel: +1 973 972 0899; Fax: +1 973 972 5594;
| |
Collapse
|
30
|
McPhillips MG, Veerapraditsin T, Cumming SA, Karali D, Milligan SG, Boner W, Morgan IM, Graham SV. SF2/ASF binds the human papillomavirus type 16 late RNA control element and is regulated during differentiation of virus-infected epithelial cells. J Virol 2004; 78:10598-605. [PMID: 15367627 PMCID: PMC516382 DOI: 10.1128/jvi.78.19.10598-10605.2004] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pre-mRNA splicing occurs in the spliceosome, which is composed of small ribonucleoprotein particles (snRNPs) and many non-snRNP components. SR proteins, so called because of their C-terminal arginine- and serine-rich domains (RS domains), are essential members of this class. Recruitment of snRNPs to 5' and 3' splice sites is mediated and promoted by SR proteins. SR proteins also bridge splicing factors across exons to help to define these units and have a central role in alternative and enhancer-dependent splicing. Here, we show that the SR protein SF2/ASF is part of a complex that forms upon the 79-nucleotide negative regulatory element (NRE) that is thought to be pivotal in posttranscriptional regulation of late gene expression in human papillomavirus type 16 (HPV-16). However, the NRE does not contain any active splice sites, is located in the viral late 3' untranslated region, and regulates RNA-processing events other than splicing. The level of expression and extent of phosphorylation of SF2/ASF are upregulated with epithelial differentiation, as is subcellular distribution, specifically in HPV-16-infected epithelial cells, and expression levels are controlled, at least in part, by the virus transcription regulator E2.
Collapse
Affiliation(s)
- Maria G McPhillips
- Institute of Biomedical and Life Sciences, Division of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, Scotland, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Park NJ, Tsao DC, Martinson HG. The two steps of poly(A)-dependent termination, pausing and release, can be uncoupled by truncation of the RNA polymerase II carboxyl-terminal repeat domain. Mol Cell Biol 2004; 24:4092-103. [PMID: 15121832 PMCID: PMC400489 DOI: 10.1128/mcb.24.10.4092-4103.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The carboxyl-terminal repeat domain (CTD) of RNA polymerase II is thought to help coordinate events during RNA metabolism. The mammalian CTD consists of 52 imperfectly repeated heptads followed by 10 additional residues at the C terminus. The CTD is required for cleavage and polyadenylation in vitro. We studied poly(A)-dependent termination in vivo using CTD truncation mutants. Poly(A)-dependent termination occurs in two steps, pause and release. We found that the CTD is required for release, the first 25 heptads being sufficient. Neither the final 10 amino acids nor the variant heptads of the second half of the CTD were required. No part of the CTD was required for poly(A)-dependent pausing--the poly(A) signal could communicate directly with the body of the polymerase. By removing the CTD, pausing could be observed without being obscured by release. Poly(A)-dependent pausing appeared to operate by slowing down the polymerase, such as by down-regulation of a positive elongation factor. Although the first 25 heptads supported undiminished poly(A)-dependent termination, they did not efficiently support events near the promoter involved in abortive elongation. However, the second half of the CTD, including the final 10 amino acids, was sufficient for these functions.
Collapse
Affiliation(s)
- Noh Jin Park
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095-1569, USA
| | | | | |
Collapse
|
32
|
Teplyakov A, Obmolova G, Bir N, Reddy P, Howard AJ, Gilliland GL. Crystal structure of the YajQ protein from Haemophilus influenzae reveals a tandem of RNP-like domains. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2004; 4:1-9. [PMID: 12943362 DOI: 10.1023/a:1024620416876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A hypothetical protein encoded by the gene YajQ of Haemophilus influenzae was selected, as part of a structural genomics project, for X-ray crystallographic structure determination and analysis to assist with the functional assignment. The protein is present in most bacteria, but not in archaea or eukaryotes. The amino acid sequence has no homology to that of other proteins. The YajQ protein was cloned, expressed, and the crystal structure determined at 2.1-A resolution by applying the multiwavelength anomalous dispersion method to a mercury derivative. The polypeptide chain is folded into two domains with identical folding topology. Each domain has a four-stranded antiparallel beta-sheet flanked on one side by two alpha-helices. This structural motif is a characteristic feature of many RNA-binding proteins. The tetrameric structure observed in the crystal suggests a possibility of binding two stretches of double-stranded nucleic acid.
Collapse
Affiliation(s)
- Alexey Teplyakov
- Center for Advanced Research in Biotechnology of the University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
| | | | | | | | | | | |
Collapse
|
33
|
Qiu J, Pintel DJ. Alternative Polyadenylation of Adeno-associated Virus Type 5 RNA within an Internal Intron Is Governed by the Distance between the Promoter and the Intron and Is Inhibited by U1 Small Nuclear RNP Binding to the Intervening Donor. J Biol Chem 2004; 279:14889-98. [PMID: 14749332 DOI: 10.1074/jbc.m312734200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adeno-associated virus type 5 is unique among adeno-associated virus serotypes in that it uses a polyadenylation site in the center of the genome. The great majority of transcripts generated from the upstream P7 and P19 promoters are polyadenylated at a site in the central intron ((pA)p); however, most of the viral transcripts generated by the proximal P41 promoter are polyadenylated at the distal polyadenylation site at the 3' end of the genome (pA)d and subsequently spliced. Polyadenylation at (pA)p increases as the distance between the RNA initiation site and the intron and (pA)p site is increased. The steady-state level of RNAs polyadenylated at (pA)p is independent of the promoter used or of the intervening sequence but is dependent upon competition with splicing, inhibition by U1 snRNP binding to the intron donor, and the intrinsic efficiency of the cleavage/polyadenylation reaction. Each of these determinants shows a marked dependence on the distance between the RNA initiation site and the intron and (pA)p. Finally, unlike other reported systems, inhibition of (pA)p by U1 snRNP binding to the intron donor is decreased as the distance between the donor and (pA)p is increased.
Collapse
Affiliation(s)
- Jianming Qiu
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, Missouri 65212, USA
| | | |
Collapse
|
34
|
McClain MT, Lutz CS, Kaufman KM, Faig OZ, Gross TF, James JA. Structural availability influences the capacity of autoantigenic epitopes to induce a widespread lupus-like autoimmune response. Proc Natl Acad Sci U S A 2004; 101:3551-6. [PMID: 14988508 PMCID: PMC373500 DOI: 10.1073/pnas.0306267101] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Indexed: 11/18/2022] Open
Abstract
A subset of lupus patients with severe nephritis and anti-nRNP reactivity produces autoantibodies primarily against two major epitopes of the nRNP A (also known as U1A) protein. These sequences span amino acids 44-56 (A3) and amino acids 103-115 (A6). These two epitopes represent structurally different regions of the protein, as both epitopes are located on the surface, but the A6 epitope is functionally masked in vivo by binding between nRNP A and the U1 RNA. Rabbits were immunized with either the A3 or A6 peptides constructed on a branching polylysine backbone. Rabbits immunized with each of these peptides first developed antibodies directed against the peptide of immunization. With boosting, the immune response of rabbits immunized with the A3 peptide spread to other common antigenic regions of nRNP A. These regions of nRNP A bound by A3 immunized rabbits are very similar to common epitopes in human systemic lupus erythematosus. These A3 immunized rabbits also develop antibodies to common antigenic regions of nRNP 70K, nRNP C, Sm B/B', and Sm D1 proteins, as well as clinical symptoms of systemic lupus erythematosus such as leukopenia and renal insufficiency. On the other hand, rabbits immunized with the A6 peptide only develop antibodies to the peptide of immunization. Anti-A3, but not anti-A6, antibodies are capable of immunoprecipitating native small nuclear ribonucleoprotein complexes. Immunization with the A3 peptide of nRNP A (a surface epitope), but not the A6 peptide (masked), induces an extensive, varied immune response against multiple small nuclear ribonucleoprotein autoantigens similar to that seen in human systemic lupus erythematosus.
Collapse
Affiliation(s)
- Micah T McClain
- Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, and Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
| | | | | | | | | | | |
Collapse
|
35
|
Kaufmann I, Martin G, Friedlein A, Langen H, Keller W. Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase. EMBO J 2004; 23:616-26. [PMID: 14749727 PMCID: PMC1271804 DOI: 10.1038/sj.emboj.7600070] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Accepted: 12/17/2003] [Indexed: 11/09/2022] Open
Abstract
In mammals, polyadenylation of mRNA precursors (pre-mRNAs) by poly(A) polymerase (PAP) depends on cleavage and polyadenylation specificity factor (CPSF). CPSF is a multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal. Based on sequence similarity to the Saccharomyces cerevisiae polyadenylation factor Fip1p, we have identified human Fip1 (hFip1) and found that the protein is an integral subunit of CPSF. hFip1 interacts with PAP and has an arginine-rich RNA-binding motif that preferentially binds to U-rich sequence elements on the pre-mRNA. Recombinant hFip1 is sufficient to stimulate the in vitro polyadenylation activity of PAP in a U-rich element-dependent manner. hFip1, CPSF160 and PAP form a ternary complex in vitro, suggesting that hFip1 and CPSF160 act together in poly(A) site recognition and in cooperative recruitment of PAP to the RNA. These results show that hFip1 significantly contributes to CPSF-mediated stimulation of PAP activity.
Collapse
Affiliation(s)
- Isabelle Kaufmann
- Department of Cell Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Georges Martin
- Department of Cell Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Arno Friedlein
- Roche Genetics, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Hanno Langen
- Roche Genetics, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Walter Keller
- Department of Cell Biology, Biozentrum, University of Basel, Basel, Switzerland
- Department of Cell Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland. Tel.: +41 61 267 20 60; Fax: +41 61 267 20 79; E-mail:
| |
Collapse
|
36
|
Kim SJ, Martinson HG. Poly(A)-dependent transcription termination: continued communication of the poly(A) signal with the polymerase is required long after extrusion in vivo. J Biol Chem 2003; 278:41691-701. [PMID: 12933817 DOI: 10.1074/jbc.m306304200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genes encoding polyadenylated mRNAs depend on their poly(A) signals for termination of transcription. An unsolved problem is how the poly(A) signal triggers the polymerase to terminate. A popular model is that this occurs during extrusion of the poly(A) signal, at which time it interacts with factors on the transcription complex. To test this idea we used cis-antisense inhibition in vivo to probe the temporal relationship between poly(A) signal extrusion and the commitment of the polymerase to terminate. Our rationale was to inactivate the poly(A) signal at increasing times post-extrusion to determine the point beyond which it is no longer required for termination. We found that communication with the polymerase is not temporally restricted to the time of poly(A) signal extrusion, but is ongoing and perhaps random. Some polymerases terminate almost immediately. Others have yet to receive their termination instructions from the poly(A) signal even 500 bp downstream, as indicated by the ability of an antisense at this distance to block termination. Thus, the poly(A) signal can functionally interact with the polymerase at considerable distances down the template. This is consistent with the emerging picture of a processing apparatus that assembles and matures while riding with the polymerase.
Collapse
Affiliation(s)
- Steven J Kim
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095-1569, USA
| | | |
Collapse
|
37
|
Sanford JR, Longman D, Cáceres JF. Multiple roles of the SR protein family in splicing regulation. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2003; 31:33-58. [PMID: 12494762 DOI: 10.1007/978-3-662-09728-1_2] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- J R Sanford
- MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK
| | | | | |
Collapse
|
38
|
Milcarek C, Martincic K, Chung-Ganster LH, Lutz CS. The snRNP-associated U1A levels change following IL-6 stimulation of human B-cells. Mol Immunol 2003; 39:809-14. [PMID: 12617996 DOI: 10.1016/s0161-5890(02)00263-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The U1A protein can be found both in a small-ribonucleoprotein particle (snRNP) that contains U1 RNA, or in a distinctive fraction, free of the snRNP, the SF-A complex. Both components have been shown to influence post- or co-transcriptional RNA processing reactions in HeLa cells. Since U1A may influence the processing of the immunoglobulin heavy chain pre-mRNA in B-cells, we wanted to see if the levels of U1A in either of its two forms changed following IL-6 stimulation to IgM secretion. Using antibodies that specifically recognize the two forms of U1A, snRNP-associated and snRNP-free, we found that approximately 16% of U1A is in the SF-A form in B-cells. We measured the levels of U1A protein in its two states in human B-cell lines both by flow cytometry and exhaustive immunoprecipitations. We found a significant decrease in the amount of snRNP-associated U1A following cytokine stimulation that correlates with the change-over to the secretory-specific poly(A) site use in the SKW 6.4 cell line. Meanwhile, the number of U1A molecules in the SF-A fraction of the pool remains nearly constant following induction to secretion. Our results suggest that the changing level of U1A in the snRNP fraction may be important for influencing Ig heavy chain mRNA processing.
Collapse
Affiliation(s)
- Christine Milcarek
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
| | | | | | | |
Collapse
|
39
|
Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res 2003; 31:1375-86. [PMID: 12595544 PMCID: PMC149834 DOI: 10.1093/nar/gkg241] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2002] [Accepted: 01/13/2003] [Indexed: 01/06/2023] Open
Abstract
Primary, secondary and higher-order structures of downstream elements of mammalian pre-mRNA polyadenylation signals [poly(A) signals] are re viewed. We have carried out a detailed analysis on our database of 244 human pre-mRNA poly(A) signals in order to characterize elements in their downstream regions. We suggest that the downstream region of the mammalian pre-mRNA poly(A) signal consists of various simple elements located at different distances from each other. Thus, the downstream region is not described by any precise consensus. Searching our database, we found that approximately 80% of pre-mRNAs with the AAUAAA or AUUAAA core upstream elements contain simple downstream elements, consisting of U-rich and/or 2GU/U tracts, the former occurring approximately 2-fold more often than the latter. Approximately one-third of the pre-mRNAs analyzed here contain sequences that may form G-quadruplexes. A substantial number of these sequences are located immediately downstream of the poly(A) signal. A possible role of G-rich sequences in the polyadenylation process is discussed. A model of the secondary structure of the SV40 late pre-mRNA poly(A) signal downstream region is presented.
Collapse
Affiliation(s)
- Margarita I Zarudnaya
- Molecular Biophysics Department, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, vul. Zabolotnoho, Kyiv, 03143, Ukraine.
| | | | | | | |
Collapse
|
40
|
Edmonds M. A history of poly A sequences: from formation to factors to function. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2003; 71:285-389. [PMID: 12102557 DOI: 10.1016/s0079-6603(02)71046-5] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Biological polyadenylation, first recognized as an enzymatic activity, remained an orphan enzyme until poly A sequences were found on the 3' ends of eukarvotic mRNAs. Their presence in bacteria viruses and later in archeae (ref. 338) established their universality. The lack of compelling evidence for a specific function limited attention to their cellular formation. Eventually the newer techniques of molecular biology and development of accurate nuclear processing extracts showed 3' end formation to be a two-step process. Pre-mRNA was first cleaved endonucleolytically at a specific site that was followed by sequential addition of AMPs from ATP to the 3' hydroxyl group at the end of mRNA. The site of cleavage was specified by a conserved hexanucleotide, AAUAAA, from 10 to 30 nt upstream of this 3' end. Extensive purification of these two activities showed that more than 10 polypeptides were needed for mRNA 3' end formation. Most of these were in complexes involved in the cleavage step. Two of the best characterized are CstF and CPSF, while two other remain partially purified but essential. Oddly, the specific proteins involved in phosphodiester bond hydrolysis have yet to be identified. The polyadenylation step occurs within the complex of poly A polymerase and poly A-binding protein, PABII, that controls poly A length. That the cleavage complex, CPSF, is also required for this step attests to a tight coupling of the two steps of 3' and formation. The reaction reconstituted from these RNA-free purified factors correctly processes pre-mRNAs. Meaningful analysis of the role of poly A in mRNA metabolism or function was possible once quantities of these proteins most often over-expressed from cDNA clones became available. The large number needed for two simple reactions of an endonuclease, a polymerase and a sequence recognition factor, pointed to 3' end formation as a regulated process. Polyadenylation itself had appeared to require regulation in cases where two poly A sites were alternatively processed to produce mRNA coding for two different proteins. The 64-KDa subunit of CstF is now known to be a regulator of poly A site choice between two sites in the immunoglobulin heavy chain of B cells. In resting cells the site used favors the mRNA for a membrane-bound protein. Upon differentiation to plasma cells, an upstream site is used the produce a secreted form of the heavy chain. Poly A site choice in the calcitonin pre-mRNA involves splicing factors at a pseudo splice site in an intron downstream of the active poly site that interacts with cleavage factors for most tissues. The molecular basis for choice of the alternate site in neuronal tissue is unknown. Proteins needed for mRNA 3' end formation also participate in other RNA-processing reactions: cleavage factors bind to the C-terminal domain of RNA polymerase during transcription; splicing of 3' terminal exons is stimulated port of by cleavage factors that bind to splicing factors at 3' splice sites. nuclear ex mRNAs is linked to cleavage factors and requires the poly A II-binding protein. Most striking is the long-sought evidence for a role for poly A in translation in yeast where it provides the surface on which the poly A-binding protein assembles the factors needed for the initiation of translation. This adaptability of eukaryotic cells to use a sequence of low information content extends to bacteria where poly A serves as a site for assembly of an mRNA degradation complex in E. coli. Vaccinia virus creates mRNA poly A tails by a streamlined mechanism independent of cleavage that requires only two proteins that recognize unique poly A signals. Thus, in spite of 40 years of study of poly A sequences, this growing multiplicity of uses and even mechanisms of formation seem destined to continue.
Collapse
MESH Headings
- Adenoviridae/genetics
- Adenoviridae/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- History, 20th Century
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/history
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Vaccinia virus/genetics
- Vaccinia virus/metabolism
- Viral Proteins/genetics
- Viral Proteins/metabolism
Collapse
Affiliation(s)
- Mary Edmonds
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260, USA
| |
Collapse
|
41
|
Abstract
We have previously described a novel complex of proteins which contains the U1snRNP-A protein (U1A) but no other small nuclear ribonucleoprotein particle (snRNP) components (O'Connor et al., RNA 1997;3:1444-55). Antibodies to this novel complex inhibit both splicing and polyadenylation in vitro of a test pre-mRNA (O'Connor et al., RNA 1997;3:1444-55; Lutz et al., RNA 1998;4:1493-9). This novel complex of proteins was identified using an unusual mouse monoclonal antibody (MoAb), called MAb 12E12. We were interested to know if autoimmune patient sera were similar to this MoAb. We have discovered a novel specificity of systemic lupus erythematosus patient sera reminiscent of MAb 12E12 in that the patient serum, like 12E12, (1) does not recognize U1A when bound to U1 RNA, (2) recognizes primarily the epitopes in the amino-terminal third of the protein, including RNA recognition motif 1 (RRM1) and (3) inhibits in vitro polyadenylation. These findings may lead to the discovery of previously undescribed autoantigens as components of the novel protein complex, and may provide insight into autoimmune diseases.
Collapse
Affiliation(s)
- O Z Faig
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry - New Jersey, Newark, NJ, USA
| | | |
Collapse
|
42
|
Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Auxiliary elements of mammalian pre-mRNAs polyadenylation signals. ACTA ACUST UNITED AC 2002. [DOI: 10.7124/bc.00062e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | - D. M. Hovorun
- Institute of Molecular Biology and Genetics, NAS of Ukraine
| |
Collapse
|
43
|
Natalizio BJ, Muniz LC, Arhin GK, Wilusz J, Lutz CS. Upstream elements present in the 3'-untranslated region of collagen genes influence the processing efficiency of overlapping polyadenylation signals. J Biol Chem 2002; 277:42733-40. [PMID: 12200454 DOI: 10.1074/jbc.m208070200] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
3'-Untranslated regions (UTRs) of genes often contain key regulatory elements involved in gene expression control. A high degree of evolutionary conservation in regions of the 3'-UTR suggests important, conserved elements. In particular, we are interested in those elements involved in regulation of 3' end formation. In addition to canonical sequence elements, auxiliary sequences likely play an important role in determining the polyadenylation efficiency of mammalian pre-mRNAs. We identified highly conserved sequence elements upstream of the AAUAAA in three human collagen genes, COL1A1, COL1A2, and COL2A1, and demonstrate that these upstream sequence elements (USEs) influence polyadenylation efficiency. Mutation of the USEs decreases polyadenylation efficiency both in vitro and in vivo, and inclusion of competitor oligoribonucleotides representing the USEs specifically inhibit polyadenylation. We have also shown that insertion of a USE into a weak polyadenylation signal can enhance 3' end formation. Close inspection of the COL1A2 3'-UTR reveals an unusual feature of two closely spaced, competing polyadenylation signals. Taken together, these data demonstrate that USEs are important auxiliary polyadenylation elements in mammalian genes.
Collapse
Affiliation(s)
- Barbara J Natalizio
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey 07103, USA
| | | | | | | | | |
Collapse
|
44
|
Aissouni Y, Perez C, Calmels B, Benech PD. The cleavage/polyadenylation activity triggered by a U-rich motif sequence is differently required depending on the poly(A) site location at either the first or last 3'-terminal exon of the 2'-5' oligo(A) synthetase gene. J Biol Chem 2002; 277:35808-14. [PMID: 12082089 DOI: 10.1074/jbc.m200540200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Production of the two mRNAs encoding distinct forms of 2'-5'-oligoadenylate synthetase depends on processing that involves the recognition of alternative poly(A) sites and an internal 5'-splice site located within the first 3'-terminal exon. The resulting 1.6- and 1.8-kb mRNAs are expressed in fibroblast cell lines, whereas lymphoblastoid B cells, such as Daudi, produce only the 1.8-kb mRNA. In the present study, we have shown that the 3'-end processing at the last 3'-terminal exon occurs independently of the core poly(A) site sequence or the presence of regulatory elements. In contrast, in Daudi cells, the recognition of the poly(A) site at the first 3'-terminal exon is impaired because of an unfavorable sequence context. The 3'-end processing at this particular location requires a strong stabilization of the cleavage/polyadenylation factors, which can be achieved by the insertion of a 25-nucleotide long U-rich motif identified upstream of the last poly(A) site. Consequently, we speculate that in cells expressing the 1.6-kb mRNA, such as fibroblasts, direct or indirect participation of a specific mechanism or cell type-specific factors are required for an efficient polyadenylation at the first 3'-terminal exon.
Collapse
Affiliation(s)
- Youssef Aissouni
- U119 INSERM, Institute of Cancerology and Immunology of Marseille, 27 Boulevard Lei Roure, F-13009, Marseille, France
| | | | | | | |
Collapse
|
45
|
Scorilas A. Polyadenylate polymerase (PAP) and 3' end pre-mRNA processing: function, assays, and association with disease. Crit Rev Clin Lab Sci 2002; 39:193-224. [PMID: 12120781 DOI: 10.1080/10408360290795510] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Polyadenylate polymerase (PAP) is one of the enzymes involved in the formation of the polyadenylate tail of the 3' end of mRNA. Poly (A) tail formation is a significant component of 3' processing, a link in the chain of events, including transcription, splicing, and cleavage/polyadenylation of pre-mRNA. Transcription, capping, splicing, polyadenylation, and transport take place as coupled processes that can regulate one another. The poly(A) tail is found in almost all eukaryotic mRNA and is important in enhancing translation initiation and determining mRNA stability. Control of poly(A) tail synthesis could possibly be a key regulatory step in gene expression. PAP-specific activity values are measured by a highly sensitive assays and immunocytochemical methods. High levels of PAP activity are associated with rapidly proliferating cells, it also prevents apoptosis. Changes of PAP activity may cause a decrease in the rate of polyadenylation in the brain during epileptic seizures. Testis-specific PAP may play an important role in spermiogenesis. PAP was found to be an unfavorable prognostic factor in leukemia and breast cancer. Furthermore, measurements of PAP activity may contribute to the definition of the biological profile of tumor cells. It is crucial to know the specific target causing the elevation of serum PAP, for it to be used as a marker for disease. This review summarizes the recently accumulated knowledge on PAP including its function, assays, and association with various human diseases, and proposes future avenues for research.
Collapse
Affiliation(s)
- Andreas Scorilas
- National Center for Scientific Research Demokritos, IPC, Athens, Greece.
| |
Collapse
|
46
|
Qiu J, Pintel DJ. The adeno-associated virus type 2 Rep protein regulates RNA processing via interaction with the transcription template. Mol Cell Biol 2002; 22:3639-52. [PMID: 11997501 PMCID: PMC133835 DOI: 10.1128/mcb.22.11.3639-3652.2002] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2001] [Revised: 02/20/2002] [Accepted: 03/04/2002] [Indexed: 11/20/2022] Open
Abstract
The adeno-associated virus type 2 (AAV) large Rep proteins can act to increase the ratio of spliced to unspliced AAV RNA when they are targeted to the transcription template via a Rep binding element. The required Rep binding site is both location and orientation independent; however, Rep enhancement decreases as the distance between the promoter and the intron of the affected transcription unit increases. Only the AAV intron and an extended polyadenylation site must remain for the AAV transcription unit to manifest responsiveness to Rep. A number of promoters, when driving the AAV capsid gene transcription unit, were responsive to targeted Rep, though to various degrees. Transactivation of transcription initiation is not sufficient for the enhancement of RNA processing, because activation of the P40 transcription unit by other activators targeted to this transcription template did not result in enhancement of the ratio of spliced to unspliced AAV RNA. These results suggest that Rep may act as a trans regulator of RNA processing by modulating such functions coupled to RNA polymerase II (RNA pol II) transcription, perhaps by affecting the composition of the transcription complex either prior to or during elongation. These results reveal another way in which gene expression can be regulated by trans-acting proteins and help explain an important feature of the parvovirus life cycle.
Collapse
Affiliation(s)
- Jianming Qiu
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri 65212, USA
| | | |
Collapse
|
47
|
Lutz CS, McClain MT, Harley JB, James JA. Anti-U1A monoclonal antibodies recognize unique epitope targets of U1A which are involved in the binding of U1 RNA. J Mol Recognit 2002; 15:163-70. [PMID: 12203842 DOI: 10.1002/jmr.569] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The U1A (or nRNP A) protein is known to play a critical role in eukaryotic pre-mRNA splicing and polyadenylation. Previous studies revealed that several mouse monoclonal antibodies (MAbs) recognized U1A as part of the U1snRNP, while MAb 12E12 was unique in that it recognized an epitope that is masked when U1A is bound to U1 RNA. In order to further characterize and understand the antigenic targets of these MAbs, we undertook fine specificity epitope mapping studies. Anti-U1A MAbs 12E12 and 10E3 each recognize unique peptides from the U1A protein. Interestingly, these MAbs recognize epitopes which have been shown to be antigenic in human autoimmune diseases. When superimposed on structures of U1A derived from crystal and NMR data, the major epitope recognized by 12E12 (amino acids 103-108) localizes to the surface of the U1A molecule. The 12E12 epitope is immediately adjacent to a helix which probably reacts to U1 RNA binding by undergoing a conformational change. This modification of structure effectively masks the 12E12 epitope, thus preventing binding of the monoclonal to U1A/U1 RNA complexes. These findings suggest that the structure of the U1A protein may be different when not part of the U1snRNP.
Collapse
Affiliation(s)
- Carol S Lutz
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, NJ 07103, USA.
| | | | | | | |
Collapse
|
48
|
Abstract
Polyadenylation is the process by which most eukaryotic mRNAs form their 3' ends. It was long held that polyadenylation required the sequence AAUAAA and that 90% of mRNAs had AAUAAA within 30 nucleotides of the site of poly(A) addition. More recent studies, aided by computer analysis of sequences made available in GenBank and expressed sequence tag (EST) databases, have suggested that the actual incidence of AAUAAA is much lower, perhaps as low as 50-60%. Reproductive biologists have long recognized that a large number of mRNAs in male germ cells of mammals lack AAUAAA but are otherwise normally polyadenylated. Recent research in our laboratory has uncovered a new form of an essential polyadenylation protein, tauCstF-64, that is most highly expressed in male germ cells, and to a smaller extent in the brain, and which we propose plays a significant role in AAUAAA-independent mRNA polyadenylation in germ cells.
Collapse
Affiliation(s)
- Clinton C MacDonald
- Department of Cell Biology & Biochemistry and Southwest Cancer Center at University Medical Center, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock 79430, USA.
| | | |
Collapse
|
49
|
Fogel BL, McNally LM, McNally MT. Efficient polyadenylation of Rous sarcoma virus RNA requires the negative regulator of splicing element. Nucleic Acids Res 2002; 30:810-7. [PMID: 11809895 PMCID: PMC100303 DOI: 10.1093/nar/30.3.810] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rous sarcoma virus pre-mRNA contains an element known as the negative regulator of splicing (NRS) that acts to inhibit viral RNA splicing. The NRS binds serine/arginine-rich (SR) proteins, hnRNP H and the U1/U11 snRNPs, and appears to inhibit splicing by acting as a decoy 5' splice site. Deletions within the gag gene that encompass the NRS also lead to increased read-through past the viral polyadenylation site, suggesting a role for the NRS in promoting polyadenylation. Using NRS-specific deletions and mutations, we show here that a polyadenylation stimulatory activity maps directly to the NRS and is most likely dependent upon SR proteins and U1 and/or U11 snRNP. hnRNP H does not appear to mediate splicing control or stimulate RSV polyadenylation, since viral RNAs containing hnRNP H-specific mutations were spliced and polyadenylated normally. However, the ability of hnRNP H mutations to suppress the read-through caused by an SR protein mutation suggests the potential for hnRNP H to antagonize polyadenylation. Interestingly, disruption of splicing control closely correlated with increased read-through, indicating that a functional NRS is necessary for efficient RSV polyadenylation rather than binding of an individual factor. We propose a model in which the NRS serves to enhance polyadenylation of RSV unspliced RNA in a process analogous to the stimulation of cellular pre-mRNA polyadenylation by splicing complexes.
Collapse
Affiliation(s)
- Brent L Fogel
- Medical College of Wisconsin, Department of Microbiology and Molecular Genetics, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | | | | |
Collapse
|
50
|
Rothnie HM, Chen G, Fütterer J, Hohn T. Polyadenylation in rice tungro bacilliform virus: cis-acting signals and regulation. J Virol 2001; 75:4184-94. [PMID: 11287568 PMCID: PMC114164 DOI: 10.1128/jvi.75.9.4184-4194.2001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The polyadenylation signal of rice tungro bacilliform virus (RTBV) was characterized by mutational and deletion analysis. The cis-acting signals required to direct polyadenylation conformed to what is known for plant poly(A) signals in general and were very similar to those of the related cauliflower mosaic virus. Processing was directed by a canonical AAUAAA poly(A) signal, an upstream UG-rich region considerably enhanced processing efficiency, and sequences downstream of the cleavage site were not required. When present at the end of a transcription unit, the cis-acting signals for 3'-end processing were highly efficient in both monocot (rice) and dicot (Nicotiana plumbaginifolia) protoplasts. In a promoter-proximal position, as in the viral genome, the signal was also efficiently processed in rice protoplasts, giving rise to an abundant "short-stop" (SS-) RNA. The proportion of SS-RNA was considerably lower in N. plumbaginifolia protoplasts. In infected plants, SS-RNA was hardly detectable, suggesting either that SS-RNA is unstable in infected plants or that read-through of the promoter-proximal poly(A) site is very efficient. SS-RNA is readily detectable in transgenic rice plants (A. Klöti, C. Henrich, S. Bieri, X. He, G. Chen, P. K. Burkhardt, J. Wünn, P. Lucca, T. Hohn, I. Potrylus, and J. Fütterer, 1999. Plant Mol. Biol. 40:249-266), thus the absence of SS-RNA in infected plants can be attributed to poly(A) site bypass in the viral context to ensure production of the full-length pregenomic viral RNA. RTBV poly(A) site suppression thus depends both on context and the expression system; our results suggest that the circular viral minichromosome directs assembly of a transcription-processing complex with specific properties to effect read-through of the promoter-proximal poly(A) signal.
Collapse
Affiliation(s)
- H M Rothnie
- Friedrich Miescher Institute, CH-4002 Basel, Switzerland.
| | | | | | | |
Collapse
|