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Blake D, Gazzara MR, Breuer I, Ferretti M, Lynch KW. Alternative 3'UTR expression induced by T cell activation is regulated in a temporal and signal dependent manner. Sci Rep 2024; 14:10987. [PMID: 38745101 PMCID: PMC11094061 DOI: 10.1038/s41598-024-61951-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/12/2024] [Indexed: 05/16/2024] Open
Abstract
The length of 3' untranslated regions (3'UTR) is highly regulated during many transitions in cell state, including T cell activation, through the process of alternative polyadenylation (APA). However, the regulatory mechanisms and functional consequences of APA remain largely unexplored. Here we present a detailed analysis of the temporal and condition-specific regulation of APA following activation of primary human CD4+ T cells. We find that global APA changes are regulated temporally and CD28 costimulatory signals enhance a subset of these changes. Most APA changes upon T cell activation involve 3'UTR shortening, although a set of genes enriched for function in the mTOR pathway exhibit 3'UTR lengthening. While upregulation of the core polyadenylation machinery likely induces 3'UTR shortening following prolonged T cell stimulation; a significant program of APA changes occur prior to cellular proliferation or upregulation of the APA machinery. Motif analysis suggests that at least a subset of these early changes in APA are driven by upregulation of RBM3, an RNA-binding protein which competes with the APA machinery for binding. Together this work expands our understanding of the impact and mechanisms of APA in response to T cell activation and suggests new mechanisms by which APA may be regulated.
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Affiliation(s)
- Davia Blake
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Genomic and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Isabel Breuer
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Genetics and Epigenetics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Max Ferretti
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Genomic and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Genetics and Epigenetics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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2
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Gallicchio L, Olivares GH, Berry CW, Fuller MT. Regulation and function of alternative polyadenylation in development and differentiation. RNA Biol 2023; 20:908-925. [PMID: 37906624 PMCID: PMC10730144 DOI: 10.1080/15476286.2023.2275109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Alternative processing of nascent mRNAs is widespread in eukaryotic organisms and greatly impacts the output of gene expression. Specifically, alternative cleavage and polyadenylation (APA) is a co-transcriptional molecular process that switches the polyadenylation site (PAS) at which a nascent mRNA is cleaved, resulting in mRNA isoforms with different 3'UTR length and content. APA can potentially affect mRNA translation efficiency, localization, stability, and mRNA seeded protein-protein interactions. APA naturally occurs during development and cellular differentiation, with around 70% of human genes displaying APA in particular tissues and cell types. For example, neurons tend to express mRNAs with long 3'UTRs due to preferential processing at PASs more distal than other PASs used in other cell types. In addition, changes in APA mark a variety of pathological states, including many types of cancer, in which mRNAs are preferentially cleaved at more proximal PASs, causing expression of mRNA isoforms with short 3'UTRs. Although APA has been widely reported, both the function of APA in development and the mechanisms that regulate the choice of 3'end cut sites in normal and pathogenic conditions are still poorly understood. In this review, we summarize current understanding of how APA is regulated during development and cellular differentiation and how the resulting change in 3'UTR content affects multiple aspects of gene expression. With APA being a widespread phenomenon, the advent of cutting-edge scientific techniques and the pressing need for in-vivo studies, there has never been a better time to delve into the intricate mechanisms of alternative cleavage and polyadenylation.
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Affiliation(s)
- Lorenzo Gallicchio
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
| | - Gonzalo H. Olivares
- Escuela de Kinesiología, Facultad de Medicina y Ciencias de la Salud, Center for Integrative Biology (CIB), Universidad Mayor, Chile and Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | | | - Margaret T. Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
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3
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Agarwal V, Lopez-Darwin S, Kelley DR, Shendure J. The landscape of alternative polyadenylation in single cells of the developing mouse embryo. Nat Commun 2021; 12:5101. [PMID: 34429411 PMCID: PMC8385098 DOI: 10.1038/s41467-021-25388-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
3′ untranslated regions (3′ UTRs) post-transcriptionally regulate mRNA stability, localization, and translation rate. While 3′-UTR isoforms have been globally quantified in limited cell types using bulk measurements, their differential usage among cell types during mammalian development remains poorly characterized. In this study, we examine a dataset comprising ~2 million nuclei spanning E9.5–E13.5 of mouse embryonic development to quantify transcriptome-wide changes in alternative polyadenylation (APA). We observe a global lengthening of 3′ UTRs across embryonic stages in all cell types, although we detect shorter 3′ UTRs in hematopoietic lineages and longer 3′ UTRs in neuronal cell types within each stage. An analysis of RNA-binding protein (RBP) dynamics identifies ELAV-like family members, which are concomitantly induced in neuronal lineages and developmental stages experiencing 3′-UTR lengthening, as putative regulators of APA. By measuring 3′-UTR isoforms in an expansive single cell dataset, our work provides a transcriptome-wide and organism-wide map of the dynamic landscape of alternative polyadenylation during mammalian organogenesis. Alternative polyadenylation regulates localization, half-life and translation of mRNA isoforms. Here the authors investigate alternative polyadenylation using single cell RNA sequencing data from mouse embryos and identify 3’-UTR isoforms that are regulated across cell types and developmental time.
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Affiliation(s)
| | | | | | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. .,Howard Hughes Medical Institute, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA. .,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
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4
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Gorukmez O, Gorukmez O. First Infertile Case with CSTF2TGene Mutation. Mol Syndromol 2020; 11:228-231. [PMID: 33224017 DOI: 10.1159/000509686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
Male infertility is multifactorial and presents with heterogeneous phenotypic features. Genetic factors are responsible for up to 15% of the male infertility cases. Loss of the Cstf2t gene in male mice results in infertility. No disease-associated mutations have been described for this gene in infertile men. Here, we report a patient diagnosed with infertility in whom a homozygous nonsense mutation in the CSTF2T gene was detected by clinical exome sequencing. This case is the first description of an infertile patient who has a homozygous CSTF2T mutation.
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Affiliation(s)
- Ozlem Gorukmez
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
| | - Orhan Gorukmez
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
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5
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MacDonald CC. Tissue-specific mechanisms of alternative polyadenylation: Testis, brain, and beyond (2018 update). WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1526. [PMID: 30816016 PMCID: PMC6617714 DOI: 10.1002/wrna.1526] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/05/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Alternative polyadenylation (APA) is how genes choose different sites for 3′ end formation for mRNAs during transcription. APA often occurs in a tissue‐ or developmental stage‐specific manner that can significantly affect gene activity by changing the protein product generated, the stability of the transcript, its localization within the cell, or its translatability. Despite the important regulatory effects that APA has on tissue‐specific gene expression, only a few examples have been characterized mechanistically. In this 2018 update to our 2010 review, we examine mechanisms for the control of APA and update our understanding of the older mechanisms since 2010. We once postulated the existence of tissue‐specific factors in APA. However, while a few tissue‐specific polyadenylation factors are known, the emerging conclusion is that the majority of APA is accomplished by altering levels of core polyadenylation proteins. Examples of those core proteins include CSTF2, CPSF1, and subunits of mammalian cleavage factor I. But despite support for these mechanisms, no one has yet documented any of these proteins changing in either a tissue‐specific or developmental manner. Given the profound effect that APA can have on gene expression and human health, improved understanding of tissue‐specific APA could lead to numerous advances in gene activity control. This article is categorized under:RNA Processing > 3′ End Processing RNA in Disease and Development > RNA in Development
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Affiliation(s)
- Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
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Carew NT, Nelson AM, Liang Z, Smith SM, Milcarek C. Linking Endoplasmic Reticular Stress and Alternative Splicing. Int J Mol Sci 2018; 19:ijms19123919. [PMID: 30544499 PMCID: PMC6321306 DOI: 10.3390/ijms19123919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
RNA splicing patterns in antibody-secreting cells are shaped by endoplasmic reticulum stress, ELL2 (eleven-nineteen lysine-rich leukemia gene 2) induction, and changes in the levels of snRNAs. Endoplasmic reticulum stress induces the unfolded protein response comprising a highly conserved set of genes crucial for cell survival; among these is Ire1, whose auto-phosphorylation drives it to acquire a regulated mRNA decay activity. The mRNA-modifying function of phosphorylated Ire1 non-canonically splices Xbp1 mRNA and yet degrades other cellular mRNAs with related motifs. Naïve splenic B cells will activate Ire1 phosphorylation early on after lipopolysaccharide (LPS) stimulation, within 18 h; large-scale changes in mRNA content and splicing patterns result. Inhibition of the mRNA-degradation function of Ire1 is correlated with further differences in the splicing patterns and a reduction in the mRNA factors for snRNA transcription. Some of the >4000 splicing changes seen at 18 h after LPS stimulation persist into the late stages of antibody secretion, up to 72 h. Meanwhile some early splicing changes are supplanted by new splicing changes introduced by the up-regulation of ELL2, a transcription elongation factor. ELL2 is necessary for immunoglobulin secretion and does this by changing mRNA processing patterns of immunoglobulin heavy chain and >5000 other genes.
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Affiliation(s)
- Nolan T Carew
- School of Medicine, Department of Immunology, University of Pittsburgh, E1059 Biomedical Science Tower, Pittsburgh, PA 15261, USA.
| | - Ashley M Nelson
- School of Medicine, Department of Immunology, University of Pittsburgh, E1059 Biomedical Science Tower, Pittsburgh, PA 15261, USA.
| | - Zhitao Liang
- School of Medicine, Department of Immunology, University of Pittsburgh, E1059 Biomedical Science Tower, Pittsburgh, PA 15261, USA.
| | - Sage M Smith
- School of Medicine, Department of Immunology, University of Pittsburgh, E1059 Biomedical Science Tower, Pittsburgh, PA 15261, USA.
| | - Christine Milcarek
- School of Medicine, Department of Immunology, University of Pittsburgh, E1059 Biomedical Science Tower, Pittsburgh, PA 15261, USA.
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7
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Nelson AM, Carew NT, Smith SM, Milcarek C. RNA Splicing in the Transition from B Cells to Antibody-Secreting Cells: The Influences of ELL2, Small Nuclear RNA, and Endoplasmic Reticulum Stress. THE JOURNAL OF IMMUNOLOGY 2018; 201:3073-3083. [PMID: 30297340 DOI: 10.4049/jimmunol.1800557] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/07/2018] [Indexed: 12/21/2022]
Abstract
In the transition from B cells to Ab-secreting cells (ASCs) many genes are induced, such as ELL2, Irf4, Prdm1, Xbp1, whereas other mRNAs do not change in abundance. Nonetheless, using splicing array technology and mouse splenic B cells plus or minus LPS, we found that induced and "uninduced" genes can show large differences in splicing patterns between the cell stages, which could influence ASC development. We found that ∼55% of these splicing changes depend on ELL2, a transcription elongation factor that influences expression levels and splicing patterns of ASC signature genes, genes in the cell-cycle and N-glycan biosynthesis and processing pathways, and the secretory versus membrane forms of the IgH mRNA. Some of these changes occur when ELL2 binds directly to the genes encoding those mRNAs, whereas some of the changes are indirect. To attempt to account for the changes that occur in RNA splicing before or without ELL2 induction, we examined the amount of the small nuclear RNA molecules and found that they were significantly decreased within 18 h of LPS stimulation and stayed low until 72 h. Correlating with this, at 18 h after LPS, endoplasmic reticulum stress and Ire1 phosphorylation are induced. Inhibiting the regulated Ire1-dependent mRNA decay with 4u8C correlates with the reduction in small nuclear RNA and changes in the normal splicing patterns at 18 h. Thus, we conclude that the RNA splicing patterns in ASCs are shaped early by endoplasmic reticulum stress and Ire1 phosphorylation and later by ELL2 induction.
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Affiliation(s)
- Ashley M Nelson
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Nolan T Carew
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Sage M Smith
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Christine Milcarek
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261
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8
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The Cstf2t Polyadenylation Gene Plays a Sex-Specific Role in Learning Behaviors in Mice. PLoS One 2016; 11:e0165976. [PMID: 27812195 PMCID: PMC5094787 DOI: 10.1371/journal.pone.0165976] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/20/2016] [Indexed: 11/19/2022] Open
Abstract
Polyadenylation is an essential mechanism for the processing of mRNA 3′ ends. CstF-64 (the 64,000 Mr subunit of the cleavage stimulation factor; gene symbol Cstf2) is an RNA-binding protein that regulates mRNA polyadenylation site usage. We discovered a paralogous form of CstF-64 called τCstF-64 (Cstf2t). The Cstf2t gene is conserved in all eutherian mammals including mice and humans, but the τCstF-64 protein is expressed only in a subset of mammalian tissues, mostly testis and brain. Male mice that lack Cstf2t (Cstf2t-/- mice) experience disruption of spermatogenesis and are infertile, although female fertility is unaffected. However, a role for τCstF-64 in the brain has not yet been determined. Given the importance of RNA polyadenylation and splicing in neuronal gene expression, we chose to test the hypothesis that τCstF-64 is important for brain function. Male and female 185-day old wild type and Cstf2t-/- mice were examined for motor function, general activity, learning, and memory using rotarod, open field activity, 8-arm radial arm maze, and Morris water maze tasks. Male wild type and Cstf2t-/- mice did not show differences in learning and memory. However, female Cstf2t-/- mice showed significantly better retention of learned maze tasks than did female wild type mice. These results suggest that τCstf-64 is important in memory function in female mice. Interestingly, male Cstf2t-/- mice displayed less thigmotactic behavior than did wild type mice, suggesting that Cstf2t may play a role in anxiety in males. Taken together, our studies highlight the importance of mRNA processing in cognition and behavior as well as their established functions in reproduction.
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9
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Salem TZ, Seaborn CP, Turney CM, Xue J, Shang H, Cheng XW. The Influence of SV40 polyA on Gene Expression of Baculovirus Expression Vector Systems. PLoS One 2015; 10:e0145019. [PMID: 26659470 PMCID: PMC4686012 DOI: 10.1371/journal.pone.0145019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/25/2015] [Indexed: 01/17/2023] Open
Abstract
The simian virus 40 polyadenylation signal (SV40 polyA) has been routinely inserted downstream of the polyhedrin promoter in many baculovirus expression vector systems (BEVS). In the baculovirus prototype Autographa californica multiple nucleopolyhedrovirus (AcMNPV), the polyhedrin promoter (very late promoter) transcribes its gene by a viral RNA polymerase therefore there is no supporting evidence that SV40 polyA is required for the proper gene expression under the polyhedrin promoter. Moreover, the effect of the SV40 polyA sequence on the polyhedrin promoter activity has not been tested either at its natural polyhedrin locus or in other loci in the viral genome. In order to test the significance of adding the SV40 polyA sequence on gene expression, the expression of the enhanced green fluorescent protein (egfp) was evaluated with and without the presence of SV40 polyA under the control of the polyhedrin promoter at different genomic loci (polyherin, ecdysteroid UDP-glucosyltransferase (egt), and gp37). In this study, spectrofluorometry and western blot showed reduction of EGFP protein for all recombinant viruses with SV40 polyA, whereas qPCR showed an increase in the egfp mRNA levels. Therefore, we conclude that SV40 polyA increases mRNA levels but decreases protein production in the BEVS when the polyhedrin promoter is used at different loci. This work suggests that SV40 polyA in BEVSs should be replaced by an AcMNPV late gene polyA for optimal protein production or left untouched for optimal RNA production (RNA interference applications).
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Affiliation(s)
- Tamer Z. Salem
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
- Biomedical Sciences, University of Science and Technology at Zewail City, Giza, Egypt
- Department of Microbial Molecular Biology, AGERI, ARC, Giza, Egypt
- * E-mail: (TZS); (XC)
| | - Craig P. Seaborn
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
| | - Colin M. Turney
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
| | - Jianli Xue
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
| | - Hui Shang
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
| | - Xiao-Wen Cheng
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, Ohio, United States of America
- * E-mail: (TZS); (XC)
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Davis R, Shi Y. The polyadenylation code: a unified model for the regulation of mRNA alternative polyadenylation. J Zhejiang Univ Sci B 2015; 15:429-37. [PMID: 24793760 DOI: 10.1631/jzus.b1400076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The majority of eukaryotic genes produce multiple mRNA isoforms with distinct 3' ends through a process called mRNA alternative polyadenylation (APA). Recent studies have demonstrated that APA is dynamically regulated during development and in response to environmental stimuli. A number of mechanisms have been described for APA regulation. In this review, we attempt to integrate all the known mechanisms into a unified model. This model not only explains most of previous results, but also provides testable predictions that will improve our understanding of the mechanistic details of APA regulation. Finally, we briefly discuss the known and putative functions of APA regulation.
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Affiliation(s)
- Ryan Davis
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
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11
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Beisang D, Reilly C, Bohjanen PR. Alternative polyadenylation regulates CELF1/CUGBP1 target transcripts following T cell activation. Gene 2014; 550:93-100. [PMID: 25123787 PMCID: PMC4162518 DOI: 10.1016/j.gene.2014.08.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/22/2014] [Accepted: 08/10/2014] [Indexed: 01/19/2023]
Abstract
Alternative polyadenylation (APA) is an evolutionarily conserved mechanism for regulating gene expression. Transcript 3' end shortening through changes in polyadenylation site usage occurs following T cell activation, but the consequences of APA on gene expression are poorly understood. We previously showed that GU-rich elements (GREs) found in the 3' untranslated regions of select transcripts mediate rapid mRNA decay by recruiting the protein CELF1/CUGBP1. Using a global RNA sequencing approach, we found that a network of CELF1 target transcripts involved in cell division underwent preferential 3' end shortening via APA following T cell activation, resulting in decreased inclusion of CELF1 binding sites and increased transcript expression. We present a model whereby CELF1 regulates APA site selection following T cell activation through reversible binding to nearby GRE sequences. These findings provide insight into the role of APA in controlling cellular proliferation during biological processes such as development, oncogenesis and T cell activation.
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Affiliation(s)
- Daniel Beisang
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN, USA; Department of Microbiology, University of Minnesota, Minneapolis, MN, USA.
| | - Cavan Reilly
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA.
| | - Paul R Bohjanen
- Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN, USA; Department of Microbiology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
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12
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CstF64: cell cycle regulation and functional role in 3' end processing of replication-dependent histone mRNAs. Mol Cell Biol 2014; 34:4272-84. [PMID: 25266659 DOI: 10.1128/mcb.00791-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The 3' end processing of animal replication-dependent histone mRNAs is activated during G1/S-phase transition. The processing site is recognized by stem-loop binding protein and the U7 snRNP, but cleavage additionally requires a heat-labile factor (HLF), composed of cleavage/polyadenylation specificity factor, symplekin, and cleavage stimulation factor 64 (CstF64). Although HLF has been shown to be cell cycle regulated, the mechanism of this regulation is unknown. Here we show that levels of CstF64 increase toward the S phase and its depletion affects histone RNA processing, S-phase progression, and cell proliferation. Moreover, analyses of the interactions between CstF64, symplekin, and the U7 snRNP-associated proteins FLASH and Lsm11 indicate that CstF64 is important for recruiting HLF to histone precursor mRNA (pre-mRNA)-resident proteins. Thus, CstF64 is central to the function of HLF and appears to be at least partly responsible for its cell cycle regulation. Additionally, we show that misprocessed histone transcripts generated upon CstF64 depletion mainly accumulate in the nucleus, where they are targets of the exosome machinery, while a small cytoplasmic fraction is partly associated with polysomes.
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13
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Youngblood BA, Grozdanov PN, MacDonald CC. CstF-64 supports pluripotency and regulates cell cycle progression in embryonic stem cells through histone 3' end processing. Nucleic Acids Res 2014; 42:8330-42. [PMID: 24957598 PMCID: PMC4117776 DOI: 10.1093/nar/gku551] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Embryonic stem cells (ESCs) exhibit a unique cell cycle with a shortened G1 phase that supports their pluripotency, while apparently buffering them against pro-differentiation stimuli. In ESCs, expression of replication-dependent histones is a main component of this abbreviated G1 phase, although the details of this mechanism are not well understood. Similarly, the role of 3' end processing in regulation of ESC pluripotency and cell cycle is poorly understood. To better understand these processes, we examined mouse ESCs that lack the 3' end-processing factor CstF-64. These ESCs display slower growth, loss of pluripotency and a lengthened G1 phase, correlating with increased polyadenylation of histone mRNAs. Interestingly, these ESCs also express the τCstF-64 paralog of CstF-64. However, τCstF-64 only partially compensates for lost CstF-64 function, despite being recruited to the histone mRNA 3' end-processing complex. Reduction of τCstF-64 in CstF-64-deficient ESCs results in even greater levels of histone mRNA polyadenylation, suggesting that both CstF-64 and τCstF-64 function to inhibit polyadenylation of histone mRNAs. These results suggest that CstF-64 plays a key role in modulating the cell cycle in ESCs while simultaneously controlling histone mRNA 3' end processing.
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Affiliation(s)
- Bradford A Youngblood
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA
| | - Petar N Grozdanov
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA
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14
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Zheng D, Tian B. RNA-binding proteins in regulation of alternative cleavage and polyadenylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:97-127. [PMID: 25201104 DOI: 10.1007/978-1-4939-1221-6_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Almost all eukaryotic pre-mRNAs are processed at the 3' end by the cleavage and polyadenylation (C/P) reaction, which preludes termination of transcription and gives rise to the poly(A) tail of mature mRNA. Genomic studies in recent years have indicated that most eukaryotic mRNA genes have multiple cleavage and polyadenylation sites (pAs), leading to alternative cleavage and polyadenylation (APA) products. APA isoforms generally differ in their 3' untranslated regions (3' UTRs), but can also have different coding sequences (CDSs). APA expands the repertoire of transcripts expressed from the genome, and is highly regulated under various physiological and pathological conditions. Growing lines of evidence have shown that RNA-binding proteins (RBPs) play important roles in regulation of APA. Some RBPs are part of the machinery for C/P; others influence pA choice through binding to adjacent regions. In this chapter, we review cis elements and trans factors involved in C/P, the significance of APA, and increasingly elucidated roles of RBPs in APA regulation. We also discuss analysis of APA using transcriptome-wide techniques as well as molecular biology approaches.
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Affiliation(s)
- Dinghai Zheng
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, 185 South Orange Ave., Newark, NJ, 07103, USA
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Rehfeld A, Plass M, Krogh A, Friis-Hansen L. Alterations in polyadenylation and its implications for endocrine disease. Front Endocrinol (Lausanne) 2013; 4:53. [PMID: 23658553 PMCID: PMC3647115 DOI: 10.3389/fendo.2013.00053] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/22/2013] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Polyadenylation is the process in which the pre-mRNA is cleaved at the poly(A) site and a poly(A) tail is added - a process necessary for normal mRNA formation. Genes with multiple poly(A) sites can undergo alternative polyadenylation (APA), producing distinct mRNA isoforms with different 3' untranslated regions (3' UTRs) and in some cases different coding regions. Two thirds of all human genes undergo APA. The efficiency of the polyadenylation process regulates gene expression and APA plays an important part in post-transcriptional regulation, as the 3' UTR contains various cis-elements associated with post-transcriptional regulation, such as target sites for micro-RNAs and RNA-binding proteins. Implications of alterations in polyadenylation for endocrine disease: Alterations in polyadenylation have been found to be causative of neonatal diabetes and IPEX (immune dysfunction, polyendocrinopathy, enteropathy, X-linked) and to be associated with type I and II diabetes, pre-eclampsia, fragile X-associated premature ovarian insufficiency, ectopic Cushing syndrome, and many cancer diseases, including several types of endocrine tumor diseases. PERSPECTIVES Recent developments in high-throughput sequencing have made it possible to characterize polyadenylation genome-wide. Antisense elements inhibiting or enhancing specific poly(A) site usage can induce desired alterations in polyadenylation, and thus hold the promise of new therapeutic approaches. SUMMARY This review gives a detailed description of alterations in polyadenylation in endocrine disease, an overview of the current literature on polyadenylation and summarizes the clinical implications of the current state of research in this field.
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Affiliation(s)
- Anders Rehfeld
- Genomic Medicine, Rigshospitalet, Copenhagen University HospitalCopenhagen, Denmark
| | - Mireya Plass
- Department of Biology, The Bioinformatics Centre, University of CopenhagenCopenhagen, Denmark
| | - Anders Krogh
- Department of Biology, The Bioinformatics Centre, University of CopenhagenCopenhagen, Denmark
| | - Lennart Friis-Hansen
- Genomic Medicine, Rigshospitalet, Copenhagen University HospitalCopenhagen, Denmark
- *Correspondence: Lennart Friis-Hansen, Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, 4113, Blegdamsvej 9, DK2100 Copenhagen, Denmark. e-mail:
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16
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A complex containing the CPSF73 endonuclease and other polyadenylation factors associates with U7 snRNP and is recruited to histone pre-mRNA for 3'-end processing. Mol Cell Biol 2012; 33:28-37. [PMID: 23071092 DOI: 10.1128/mcb.00653-12] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Animal replication-dependent histone pre-mRNAs are processed at the 3' end by endonucleolytic cleavage that is not followed by polyadenylation. The cleavage reaction is catalyzed by CPSF73 and depends on the U7 snRNP and its integral component, Lsm11. A critical role is also played by the 220-kDa protein FLASH, which interacts with Lsm11. Here we demonstrate that the N-terminal regions of these two proteins form a platform that tightly interacts with a unique combination of polyadenylation factors: symplekin, CstF64, and all CPSF subunits, including the endonuclease CPSF73. The interaction is inhibited by alterations in each component of the FLASH/Lsm11 complex, including point mutations in FLASH that are detrimental for processing. The same polyadenylation factors are associated with the endogenous U7 snRNP and are recruited in a U7-dependent manner to histone pre-mRNA. Collectively, our studies identify the molecular mechanism that recruits the CPSF73 endonuclease to histone pre-mRNAs, reveal an unexpected complexity of the U7 snRNP, and suggest that in animal cells polyadenylation factors assemble into two alternative complexes-one specifically crafted to generate polyadenylated mRNAs and the other to generate nonpolyadenylated histone mRNAs that end with the stem-loop.
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17
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Martin G, Gruber AR, Keller W, Zavolan M. Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. Cell Rep 2012; 1:753-63. [PMID: 22813749 DOI: 10.1016/j.celrep.2012.05.003] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/10/2012] [Accepted: 05/07/2012] [Indexed: 11/16/2022] Open
Abstract
Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we performed transcriptome-wide mapping of both binding sites of 3' end processing factors CPSF-160, CPSF-100, CPSF-73, CPSF-30, Fip1, CstF-64, CstF-64τ, CF I(m)25, CF I(m)59, and CF I(m)68 and 3' end processing sites in HEK293 cells. We found that although binding sites of these factors generally cluster around the poly(A) sites most frequently used in cleavage, CstF-64/CstF-64τ and CFI(m) proteins have much higher positional specificity compared to CPSF components. Knockdown of CF I(m)68 induced a systematic use of proximal polyadenylation sites, indicating that changes in relative abundance of a single 3' end processing factor can modulate the length of 3' untranslated regions across the transcriptome and suggesting a mechanism behind the previously observed increase in tumor cell invasiveness upon CF I(m)68 knockdown.
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Affiliation(s)
- Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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18
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Peterson ML. Immunoglobulin heavy chain gene regulation through polyadenylation and splicing competition. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 2:92-105. [PMID: 21956971 DOI: 10.1002/wrna.36] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The immunoglobulin heavy chain (IgH) genes, which encode one of the two chains of antibody molecules, were the first cellular genes shown to undergo developmentally regulated alternative RNA processing. These genes produce two different mRNAs from a single primary transcript. One mRNA is cleaved and polyadenylated at an upstream poly(A) signal while the other mRNA removes this poly(A) signal by RNA splicing and is cleaved and polyadenylated at a downstream poly(A) site. A broad range of studies have been performed to understand the mechanism of IgH RNA processing regulation during B lymphocyte development. The model that has emerged is much more complex than envisioned by the earliest view of regulation through poly(A) signal choice. Regulation requires that the IgH gene contain competing splice and cleavage-polyadenylation reactions with balanced efficiencies. Because non-IgH genes with these structural features also can be regulated, IgH gene-specific sequence elements are not required for regulation. Changes in cleavage-polyadenylation and RNA splicing, as well as pol II elongation, all contribute to IgH developmental RNA processing regulation. Multiple factors are likely involved in the regulation during B lymphocyte maturation. Additional biologically relevant factors that contribute to IgH regulation remain to be identified and incorporated into a mechanistic model for regulation. Much of the work to date confirms the complex nature of IgH mRNA regulation and suggests that a thorough understanding of this control will remain a challenge. However, it is also likely that such understanding will help elucidate novel mechanisms of RNA processing regulation.
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Affiliation(s)
- Martha L Peterson
- Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY, USA.
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19
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Santos P, Arumemi F, Park KS, Borghesi L, Milcarek C. Transcriptional and epigenetic regulation of B cell development. Immunol Res 2011; 50:105-12. [PMID: 21717070 DOI: 10.1007/s12026-011-8225-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
B cell development starts in the bone marrow where hematopoietic stem cells (HSCs) progress through sequential developmental stages, as it differentiates into a naïve B cell expressing surface immunoglobulin. In the periphery, B cells that encounter antigen can further differentiate into antibody-secreting plasma cells. In this review, we focus on two factors, E47 and ELL2, which play important roles in the regulation of B cell development in the bone marrow and differentiation of mature B cells into plasma cells in the periphery, respectively. First, E47 activity is required for B cell development in the bone marrow. In addition, we have identified a cell-intrinsic role for E47 in regulating efficient self-renewal and long-term multilineage bone marrow reconstitution potential of HSCs. Second, we explored the role of transcription elongation factors in the super elongation complex (SEC), including ELL2 (eleven-nineteen lysine-rich leukemia factor) in driving poly(A) site choice and plasma cell development. We found that elongation factors impel high levels of IgH mRNA production and alternative processing at the promoter proximal, secretory-specific (sec) poly(A) site in plasma cells by enhancing RNA polymerase II modifications and downstream events. The sec poly(A) site, essentially hidden in B cells, is found by SEC factors in plasma cells.
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Affiliation(s)
- Patricia Santos
- Department of Immunology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 15261, USA
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20
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Abstract
Manganese superoxide dismutase (MnSOD) is a nuclear encoded and mitochondrial matrix localized redox enzyme that is known to regulate cellular redox environment. Cellular redox environment changes during transitions between quiescent and proliferative cycles. Human MnSOD has two poly(A) sites resulting in two transcripts: 1.5 and 4.2 kb. The present study investigates if the 3'-untranslated region (UTR) of MnSOD regulates its expression during transitions between quiescent and proliferating cycles, and in response to radiation. A preferential increase in the 1.5 kb MnSOD transcript levels was observed in quiescent cells, while the abundance of the longer transcript showed a direct correlation with the percentage of S-phase cells. Log transformed expression ratio of the longer to shorter transcript was also higher in proliferating normal and cancer cells. Deletion and reporter assays showed a significant decrease in reporter activity in constructs carrying multiple AU-rich sequence that are present in the 3'-UTR of the longer MnSOD transcript. Overexpression of the MnSOD 3'-UTR representing the longer transcript enhanced endogenous MnSOD mRNA levels, which was associated with an increase in MnSOD protein levels and a decrease in the percentage of S-phase cells. Irradiation increases the mRNA levels of the 1.5 kb MnSOD transcript, which was consistent with a significant increase in reporter activity of the construct carrying the 3'-UTR of the shorter transcript. We conclude that the 3'-UTR of MnSOD regulates MnSOD expression in response to different growth states and radiation.
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21
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Hockert KJ, Martincic K, Mendis-Handagama SMLC, Borghesi LA, Milcarek C, Dass B, MacDonald CC. Spermatogenetic but not immunological defects in mice lacking the τCstF-64 polyadenylation protein. J Reprod Immunol 2011; 89:26-37. [PMID: 21489638 DOI: 10.1016/j.jri.2011.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/07/2011] [Accepted: 01/16/2011] [Indexed: 12/31/2022]
Abstract
Alternative polyadenylation controls expression of genes in many tissues including immune cells and male germ cells. The τCstF-64 polyadenylation protein is expressed in both cell types, and we previously showed that Cstf2t, the gene encoding τCstF-64 was necessary for spermatogenesis and fertilization. Here we examine consequences of τCstF-64 loss in both germ cells and immune cells. Spermatozoa from Cstf2t null mutant (Cstf2t(-/-)) mice of ages ranging from 60 to 108 days postpartum exhibited severe defects in motility and morphology that were correlated with a decrease in numbers of round spermatids. Spermatozoa in these mice also displayed severe morphological defects at every age, especially in the head and midpiece. In the testicular epithelium, we saw normal numbers of cells in earlier stages of spermatogenesis, but reduced numbers of round spermatids in Cstf2t(-/-) mice. Although Leydig cell numbers were normal, we did observe reduced levels of plasma testosterone in the knockout animals, suggesting that reduced androgen might also be contributing to the Cstf2t(-/-) phenotype. Finally, while τCstF-64 was expressed in a variety of immune cell types in wild type mice, we did not find differences in secreted IgG or IgM or changes in immune cell populations in Cstf2t(-/-) mice, suggesting that τCstF-64 function in immune cells is either redundant or vestigial. Together, these data show that τCstF-64 function is primarily to support spermatogenesis, but only incidentally to support immune cell function.
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Affiliation(s)
- Kathy Jo Hockert
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Texas, Lubbock, TX 79430, USA
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22
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Lim Y, Hong E, Kwon D, Lee E. Proteomic identification and comparative analysis of asymmetrically arginine-methylated proteins in immortalized, young and senescent cells. Electrophoresis 2011; 31:3823-33. [PMID: 21080485 DOI: 10.1002/elps.201000361] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein-arginine methylation is one of the modifications that yields mono and dimethyl (asymmetric or symmetric) arginine residues in proteins. Previously, we found that asymmetric arginine methylation is decreased proportionately with a decrease of cell proliferation potential of cells, and such arginine methylation is greatest in immortalized cells, followed by normal young cells, and lowest in replicatively senescent cells. Using an asymmetric dimethyl-arginine-specific antibody, we identified arginine-methylated proteins in these cell types by immunoprecipitation and 2-D immunoblotting followed by MS. As a result, arginine methylation of chaperone molecules and RNA-binding proteins was differentially regulated between immortalized or young cells and senescent cells. Immortalized cells had significantly higher levels of methyl-accepting proteins, such as cleavage stimulation factor 2 (CstF2) and heterogeneous nuclear ribonucleoprotein (hnRNP) R, than young cells. However, senescent cells contained hypomethylated CstF2, hnRNP K, and chaperone containing TCP1 subunit 7, as well as decreased hnRNP R level. Further, significant reduction of arginine modification in CstF2 and chaperone containing TCP1 subunit 7 was observed in prematurely senescent fibroblasts, induced by treatment with adenosine dialdehyde, a transmethylation inhibitor, or subcytotoxic concentration of H(2)O(2). These results suggest that asymmetric modification of RNA-binding proteins and molecular chaperones plays an essential role in maintaining cell proliferation capability.
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Affiliation(s)
- Yongchul Lim
- Cellular and Developmental Biology, Division of Brain Korea 21 Program for Biomedical Sciences, Korea University, Seoul, Korea
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23
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Ruepp MD, Schweingruber C, Kleinschmidt N, Schümperli D. Interactions of CstF-64, CstF-77, and symplekin: implications on localisation and function. Mol Biol Cell 2010; 22:91-104. [PMID: 21119002 PMCID: PMC3016980 DOI: 10.1091/mbc.e10-06-0543] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Important interactions controlling the function of CstF-64 in histone RNA processing and general mRNA cleavage/polyadenylation are identified, and an interesting coregulation of CstF-64 and its paralogue CstF-64Tau leads to a model for CstF regulation and its role in modulating poly(A) site choice. Cleavage/polyadenylation of mRNAs and 3′ processing of replication-dependent histone transcripts are both mediated by large complexes that share several protein components. Functional studies of these shared proteins are complicated by the cooperative binding of the individual subunits. For CstF-64, an additional difficulty is that symplekin and CstF-77 bind mutually exclusively to its hinge domain. Here we have identified CstF-64 and symplekin mutants that allowed us to distinguish between these interactions and to elucidate the role of CstF-64 in the two processing reactions. The interaction of CstF-64 with symplekin is limiting for histone RNA 3′ processing but relatively unimportant for cleavage/polyadenylation. In contrast, the nuclear accumulation of CstF-64 depends on its binding to CstF-77 and not to symplekin. Moreover, the CstF-64 paralogue CstF-64Tau can compensate for the loss of CstF-64. As CstF-64Tau has a lower affinity for CstF-77 than CstF-64 and is relatively unstable, it is the minor form. However, it may become up-regulated when the CstF-64 level decreases, which has biological implications for spermatogenesis and probably also for other regulatory events. Thus, the interactions between CstF-64/CstF-64Tau and CstF-77 are important for the maintenance of stoichiometric nuclear levels of the CstF complex components and for their intracellular localization, stability, and function.
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Affiliation(s)
- Marc-David Ruepp
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland
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24
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Jen CY, Lin CY, Huang BM, Leu SF. Cordycepin Induced MA-10 Mouse Leydig Tumor Cell Apoptosis through Caspase-9 Pathway. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2010; 2011:984537. [PMID: 19131393 PMCID: PMC3137878 DOI: 10.1093/ecam/nen084] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 12/05/2008] [Indexed: 01/08/2023]
Abstract
In the present study, the apoptotic effect of cordycepin on MA-10 cells, a mouse Leydig tumor cell line, was investigated. Results demonstrated that the number of rounding-up cell increased by cordycepin (10 μM to 5 mM for 24 h), and cells with plasma membrane blebbing could be observed by 100 μM cordycepin. In viability test, MA-10 cell surviving rate significantly decreased as the dosage (10 μM to 5 mM) and duration (3–24 h) of cordycepin treatment increased (P < 0.05). Cordycepin at 100 μM and 1 mM for 24 h treatment induced significant DNA fragmentation (P < 0.05). In addition, the percentage of G1 and G2/M phase cell significantly declined by cordycepin (100 μM and 1 mM) for 24 h treatment, while the percentages of subG1 phase cell increased by 100 μM and/or 1 mM cordycepin in 6, 12 and 24 h treatments (P < 0.05), respectively, which highly suggested that cordycepin induced MA-10 cell apoptosis. In mechanism study with the treatments of caspases, c-Jun NH2 terminal kinase (JNK) or reactive oxygen species (ROS) inhibitors plus cordycepin for 24 h, only caspases inhibitor suppressed subG1 phase in MA-10 cells. Moreover, western blotting results showed that cordycepin induced caspase-9, -3 and -7 protein expressions, but not caspase-8, in time- and dose-dependent manners. In conclusion, cordycepin induced apoptosis in MA-10 mouse Leydig tumor cells through a caspase-9 and -3 and -7 dependent pathway.
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Affiliation(s)
- Chun-Yi Jen
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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25
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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.
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Affiliation(s)
- Carol S Lutz
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, NJ, USA.
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26
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Singh P, Alley TL, Wright SM, Kamdar S, Schott W, Wilpan RY, Mills KD, Graber JH. Global changes in processing of mRNA 3' untranslated regions characterize clinically distinct cancer subtypes. Cancer Res 2010; 69:9422-30. [PMID: 19934316 DOI: 10.1158/0008-5472.can-09-2236] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular cancer diagnostics are an important clinical advance in cancer management, but new methods are still needed. In this context, gene expression signatures obtained by microarray represent a useful molecular diagnostic. Here, we describe novel probe-level microarray analyses that reveal connections between mRNA processing and neoplasia in multiple tumor types, with diagnostic potential. We now show that characteristic differences in mRNA processing, primarily in the 3'-untranslated region, define molecular signatures that can distinguish similar tumor subtypes with different survival characteristics, with at least 74% accuracy. Using a mouse model of B-cell leukemia/lymphoma, we find that differences in transcript isoform abundance are likely due to both alternative polyadenylation (APA) and differential degradation. While truncation of the 3'-UTR is the most common observed pattern, genes with elongated transcripts were also observed, and distinct groups of affected genes are found in related but distinct tumor types. Genes with elongated transcripts are overrepresented in ontology categories related to cell-cell adhesion and morphology. Analysis of microarray data from human primary tumor samples revealed similar phenomena. Western blot analysis of selected proteins confirms that changes in the 3'-UTR can correlate with changes in protein expression. Our work suggests that alternative mRNA processing, particularly APA, can be a powerful molecular biomarker with prognostic potential. Finally, these findings provide insights into the molecular mechanisms of gene deregulation in tumorigenesis.
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Affiliation(s)
- Priyam Singh
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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27
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Hockert JA, Yeh HJ, MacDonald CC. The hinge domain of the cleavage stimulation factor protein CstF-64 is essential for CstF-77 interaction, nuclear localization, and polyadenylation. J Biol Chem 2009; 285:695-704. [PMID: 19887456 DOI: 10.1074/jbc.m109.061705] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Because polyadenylation is essential for cell growth, in vivo examination of polyadenylation protein function has been difficult. Here we describe a new in vivo assay that allows structure-function assays on CstF-64, a protein that binds to pre-mRNAs downstream of the cleavage site for accurate and efficient polyadenylation. In this assay (the stem-loop luciferase assay for polyadenylation, SLAP), expression of a luciferase pre-mRNA with a modified downstream sequence element was made dependent upon co-expression of an MS2-CstF-64 fusion protein. We show here that SLAP accurately reflects CstF-64-dependent polyadenylation, confirming the validity of this assay. Using SLAP, we determined that CstF-64 domains involved in RNA binding, interaction with CstF-77 (the "Hinge" domain), and coupling to transcription are critical for polyadenylation. Further, we showed that the Hinge domain is necessary for CstF-64 interaction with CstF-77 and consequent nuclear localization, suggesting that nuclear import of a preformed CstF complex is an essential step in polyadenylation.
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Affiliation(s)
- J Andrew Hockert
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430-6540, USA
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28
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Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 2009; 138:673-84. [PMID: 19703394 DOI: 10.1016/j.cell.2009.06.016] [Citation(s) in RCA: 1199] [Impact Index Per Article: 79.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 04/21/2009] [Accepted: 06/09/2009] [Indexed: 01/07/2023]
Abstract
In cancer cells, genetic alterations can activate proto-oncogenes, thereby contributing to tumorigenesis. However, the protein products of oncogenes are sometimes overexpressed without alteration of the proto-oncogene. Helping to explain this phenomenon, we found that when compared to similarly proliferating nontransformed cell lines, cancer cell lines often expressed substantial amounts of mRNA isoforms with shorter 3' untranslated regions (UTRs). These shorter isoforms usually resulted from alternative cleavage and polyadenylation (APA). The APA had functional consequences, with the shorter mRNA isoforms exhibiting increased stability and typically producing ten-fold more protein, in part through the loss of microRNA-mediated repression. Moreover, expression of the shorter mRNA isoform of the proto-oncogene IGF2BP1/IMP-1 led to far more oncogenic transformation than did expression of the full-length, annotated mRNA. The high incidence of APA in cancer cells, with consequent loss of 3'UTR repressive elements, suggests a pervasive role for APA in oncogene activation without genetic alteration.
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29
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Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 2008; 320:1643-7. [PMID: 18566288 DOI: 10.1126/science.1155390] [Citation(s) in RCA: 1024] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Messenger RNA (mRNA) stability, localization, and translation are largely determined by sequences in the 3' untranslated region (3'UTR). We found a conserved increase in expression of mRNAs terminating at upstream polyadenylation sites after activation of primary murine CD4+ T lymphocytes. This program, resulting in shorter 3'UTRs, is a characteristic of gene expression during immune cell activation and correlates with proliferation across diverse cell types and tissues. Forced expression of full-length 3'UTRs conferred reduced protein expression. In some cases the reduction in protein expression could be reversed by deletion of predicted microRNA target sites in the variably included region. Our data indicate that gene expression is coordinately regulated, such that states of increased proliferation are associated with widespread reductions in the 3'UTR-based regulatory capacity of mRNAs.
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Affiliation(s)
- Rickard Sandberg
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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30
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Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 2008. [PMID: 18566288 DOI: 10.1126/science.1155390.proliferating] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
Messenger RNA (mRNA) stability, localization, and translation are largely determined by sequences in the 3' untranslated region (3'UTR). We found a conserved increase in expression of mRNAs terminating at upstream polyadenylation sites after activation of primary murine CD4+ T lymphocytes. This program, resulting in shorter 3'UTRs, is a characteristic of gene expression during immune cell activation and correlates with proliferation across diverse cell types and tissues. Forced expression of full-length 3'UTRs conferred reduced protein expression. In some cases the reduction in protein expression could be reversed by deletion of predicted microRNA target sites in the variably included region. Our data indicate that gene expression is coordinately regulated, such that states of increased proliferation are associated with widespread reductions in the 3'UTR-based regulatory capacity of mRNAs.
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Affiliation(s)
- Rickard Sandberg
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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31
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3' end mRNA processing: molecular mechanisms and implications for health and disease. EMBO J 2008; 27:482-98. [PMID: 18256699 DOI: 10.1038/sj.emboj.7601932] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 10/24/2007] [Indexed: 12/27/2022] Open
Abstract
Recent advances in the understanding of the molecular mechanism of mRNA 3' end processing have uncovered a previously unanticipated integrated network of transcriptional and RNA-processing mechanisms. A variety of human diseases impressively reflect the importance of the precision of the complex 3' end-processing machinery and gene specific deregulation of 3' end processing can result from mutations of RNA sequence elements that bind key specific processing factors. Interestingly, more general deregulation of 3' end processing can be caused either by mutations of these processing factors or by the disturbance of the well-coordinated equilibrium between these factors. From a medical perspective, both loss of function and gain of function can be functionally relevant, and an increasing number of different disease entities exemplifies that inappropriate 3' end formation of human mRNAs can have a tremendous impact on health and disease. Here, we review the mechanistic hallmarks of mRNA 3' end processing, highlight the medical relevance of deregulation of this important step of mRNA maturation and illustrate the implications for diagnostic and therapeutic strategies.
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32
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Shell SA, Martincic K, Tran J, Milcarek C. Increased phosphorylation of the carboxyl-terminal domain of RNA polymerase II and loading of polyadenylation and cotranscriptional factors contribute to regulation of the ig heavy chain mRNA in plasma cells. THE JOURNAL OF IMMUNOLOGY 2008; 179:7663-73. [PMID: 18025212 DOI: 10.4049/jimmunol.179.11.7663] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
B cells produce Ig H chain (IgH) mRNA and protein, primarily of the membrane-bound specific form. Plasma cells produce 20- to 50-fold higher amounts of IgH mRNA, most processed to the secretory specific form; this shift is mediated by substantial changes in RNA processing but only a small increase in IgH transcription rate. We investigated RNA polymerase II (RNAP-II) loading and phosphorylation of its C-terminal domain (CTD) on the IgG2a H chain gene, comparing two mouse cell lines representing B (A20) and plasma cells (AxJ) that express the identical H chain gene whose RNA is processed in different ways. Using chromatin immunoprecipitation and real-time PCR, we detected increased RNAP-II and Ser-2 and Ser-5 phosphorylation of RNAP-II CTD close to the IgH promoter in plasma cells. We detected increased association of several 3' end-processing factors, ELL2 and PC4, at the 5' end of the IgH gene in AxJ as compared with A20 cells. Polymerase progress and factor associations were inhibited by 5,6-dichlorobenzimidazole riboside, a drug that interferes with the addition of the Ser-2 to the CTD of RNAP-II. Taken together, these data indicate a role for CTD phosphorylation and polyadenylation/ELL2/PC4 factor loading on the polymerase in the choice of the secretory poly(A) site for the IgH gene.
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Affiliation(s)
- Scott A Shell
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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33
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Lee SH, Choi HS, Kim H, Lee Y. ERK is a novel regulatory kinase for poly(A) polymerase. Nucleic Acids Res 2007; 36:803-13. [PMID: 18084034 PMCID: PMC2241896 DOI: 10.1093/nar/gkm1091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Poly(A) polymerase (PAP), which adds poly(A) tails to the 3′ end of mRNA, can be phosphorylated at several sites in the C-terminal domain. Phosphorylation often mediates regulation by extracellular stimuli, suggesting PAP may be regulated by such stimuli. In this study, we found that phosphorylation of PAP was increased upon growth stimulation and that the mitogen-activated protein kinase ERK was responsible for the increase in phosphorylation. We identified serine 537 of PAP as a unique phosphorylation site by ERK. PAP phosphorylation of serine 537 by ERK increased its nonspecific polyadenylation activity in vitro. This PAP activity was also activated by stimulation of ERK with phorbol-12-myristate-13-acetate in vivo. These data suggest that ERK is a novel regulatory kinase for PAP and further, that PAP activity could be regulated by extracellular stimuli through an ERK-dependent signaling pathway(s).
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Affiliation(s)
- Seol-Hoon Lee
- Department of Chemistry and Center for Molecular Design and Synthesis, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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34
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Peterson ML. Mechanisms controlling production of membrane and secreted immunoglobulin during B cell development. Immunol Res 2007; 37:33-46. [PMID: 17496345 DOI: 10.1007/bf02686094] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/27/2022]
Abstract
The immunoglobulin gene which encodes both membrane-associated and secreted proteins through alternative RNA processing reactions has been a model system used for over 25 yr to better understand the regulatory mechanisms governing alternative RNA processing. This gene contains competing cleavage-polyadenylation and RNA splicing reactions and the relative use of the two pathways is differentially regulated between B cells and plasma cells. General cleavage-polyadenylation and RNA splicing reactions are both altered during B cell maturation to affect immunoglobulin expression. However, the specific factors involved in this regulation have yet to be identified clearly. As transcriptional regulators stimulate the developmental RNA processing switch, microarray analysis is a promising approach to identify candidate regulators of this complex RNA processing mechanism.
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Affiliation(s)
- Martha L Peterson
- Department of Microbiology, Immunology & Molecular Genetics, University of Kentucky College of Medicine, 800 Rose Street, Lexington, KY 40536, USA.
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35
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Kubo T, Wada T, Yamaguchi Y, Shimizu A, Handa H. Knock-down of 25 kDa subunit of cleavage factor Im in Hela cells alters alternative polyadenylation within 3'-UTRs. Nucleic Acids Res 2006; 34:6264-71. [PMID: 17098938 PMCID: PMC1669743 DOI: 10.1093/nar/gkl794] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Alternative polyadenylation leads to mRNAs with variable 3′ ends. Since a 3′-untranslated region (3′-UTR) often contains cis elements that impact stability or localization of mRNA or translation, selection of poly(A) sites in a 3′-UTR is regulated in mammalian cells. However, the molecular basis for alternative poly(A) site selection within a 3′-UTR has been unclear. Here we show involvement of cleavage factor Im (CFIm) in poly(A) site selection within a 3′-UTR. CFIm is a heterodimeric 3′ end-processing complex, which functions to assemble other processing factors on pre-mRNA in vitro. We knocked down 25 kDa subunit of CFIm (CFIm25) in HeLa cells and analyzed alternative poly(A) site selection of TIMP-2, syndecan2, ERCC6 and DHFR genes by northern blotting. We observed changes in the distribution of mRNAs in CFIm25 depleted cells, suggesting a role for CFIm in alternative poly(A) site selection. Furthermore, tissue specific analysis demonstrated that the CFIm25 gene gave rise to 1.1, 2.0 and 4.6 kb mRNAs. The 4.6 kb mRNA was ubiquitously expressed, while the 1.1 and 2.0 kb mRNAs were expressed in a tissue specific manner. We found three likely poly(A) sites in the CFIm25 3′-UTR, suggesting alternative polyadenylation. Our results indicate that alternative poly(A) site selection is a well-regulated process in vivo.
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Affiliation(s)
- Tomohiro Kubo
- Division of Systemic Life Science, Graduate School of BiostudiesKyoto University, Kyoto, Japan
| | - Tadashi Wada
- Graduate School of Bioscience and BiotechnologyYokohama, Japan
- Integrated Research Institute, Tokyo Institute of TechnologyYokohama, Japan
| | - Yuki Yamaguchi
- Graduate School of Bioscience and BiotechnologyYokohama, Japan
| | - Akira Shimizu
- Translational Research Center, Kyoto University HospitalKyoto, Japan
| | - Hiroshi Handa
- Graduate School of Bioscience and BiotechnologyYokohama, Japan
- To whom correspondence should be addressed. Tel: 81 45 924 5872; Fax: 81 45 924 5834;
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36
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Wu WC, Hsiao JR, Lian YY, Lin CY, Huang BM. The apoptotic effect of cordycepin on human OEC-M1 oral cancer cell line. Cancer Chemother Pharmacol 2006; 60:103-11. [PMID: 17031645 DOI: 10.1007/s00280-006-0354-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 09/09/2006] [Indexed: 11/30/2022]
Abstract
Cordycepin (3'-deoxyadenosine), a pure compound of Cordyceps sinensis, has been illustrated with anti-tumor effects. In the present study, the apoptotic effect of cordycepin on OEC-M1, a human oral squamous cancer cell line, was investigated by morphological observations, cell viability assay, annexin V-FITC analysis and flow cytometry methods. Results demonstrated that the number of rounded-up cell increased as treatment duration of cordycepin (100 microM) increased from 3 to 48 h, and the plasma membrane blebbing could be observed after 12 h treatment. In cell viability assay, cell surviving rate significantly decreased as the dosage and duration of cordycepin treatment increased (P < 0.05). Moreover, phosphatidylserine flipping on cell membrane could be detected with 3, 6 and 12 h cordycepin treatment, which indicated an early apoptotic phenomenon. Furthermore, cell cycle studies illustrated that the percentage of G1 phase cell declined as the dosages of cordycepin increased (10 microM to 5 mM), while the percentages of G2M and subG1 phase cell increased (P < 0.05) in 12, 24 and 48 h cordycepin treatment. These results further confirmed the apoptotic event. In conclusion, cordycepin significantly induced cell apoptotsis in OEC-M1 human oral squamous cancer cells.
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Affiliation(s)
- Wei-Ciao Wu
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
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37
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Jaeger S, Martin F, Rudinger-Thirion J, Giegé R, Eriani G. Binding of human SLBP on the 3'-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring. Nucleic Acids Res 2006; 34:4987-95. [PMID: 16982637 PMCID: PMC1635294 DOI: 10.1093/nar/gkl666] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In metazoans, cell-cycle-dependent histones are produced from poly(A)-lacking mRNAs. The 3′ end of histone mRNAs is formed by an endonucleolytic cleavage of longer precursors between a conserved stem–loop structure and a purine-rich histone downstream element (HDE). The cleavage requires at least two trans-acting factors: the stem–loop binding protein (SLBP), which binds to the stem–loop and the U7 snRNP, which anchors to histone pre-mRNAs by annealing to the HDE. Using RNA structure-probing techniques, we determined the secondary structure of the 3′-untranslated region (3′-UTR) of mouse histone pre-mRNAs H4–12, H1t and H2a–614. Surprisingly, the HDE is embedded in hairpin structures and is therefore not easily accessible for U7 snRNP anchoring. Probing of the 3′-UTR in complex with SLBP revealed structural rearrangements leading to an overall opening of the structure especially at the level of the HDE. Electrophoretic mobility shift assays demonstrated that the SLBP-induced opening of HDE actually facilitates U7 snRNA anchoring on the histone H4–12 pre-mRNAs 3′ end. These results suggest that initial binding of the SLBP functions in making the HDE more accessible for U7 snRNA anchoring.
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Affiliation(s)
| | | | | | | | - Gilbert Eriani
- To whom correspondence should be addressed: Tel: +33 3 88 41 70 42; Fax: +33 3 88 60 22 18;
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38
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Huber Z, Monarez RR, Dass B, MacDonald CC. The mRNA encoding tauCstF-64 is expressed ubiquitously in mouse tissues. Ann N Y Acad Sci 2006; 1061:163-72. [PMID: 16467265 DOI: 10.1196/annals.1336.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Polyadenylation is a process of endonucleolytic cleavage of the mRNA, followed by addition of up to 250 adenosine residues to the 3' end of the mRNA. Polyadenylation is essential for eukaryotic mRNA expression, and CstF-64 is a subunit of the CstF polyadenylation factor that is required for accurate polyadenylation. We discovered that there are two forms of the CstF-64 protein in mammalian male germ cells, one of which (CstF-64) is expressed in all tissues, the other of which (tauCstF-64) is expressed only in male germ cells and in brain (albeit at significantly lower levels in the brain). Therefore, we were surprised to find that, using reverse transcription-PCR, cDNA cloning, and RNA blot analyses, tauCstF-64 mRNA was expressed at higher levels in brain than in testis. Also, tauCstF-64 mRNA was expressed at lower but detectable levels in all tissues tested, including epididymis, heart, kidney, liver, lung, muscle, ovary, spleen, thymus, and uterus. These results suggest the hypothesis that tauCstF-64 mRNA is regulated at the translational or post-translational level.
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Affiliation(s)
- Zane Huber
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
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39
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Alkan S, Martincic K, Milcarek C. The hnRNPs F and H2 bind to similar sequences to influence gene expression. Biochem J 2006; 393:361-71. [PMID: 16171461 PMCID: PMC1383695 DOI: 10.1042/bj20050538] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The hnRNPs (heterogeneous nuclear ribonucleoproteins) F and H2 share a similar protein structure. Both have been implicated as regulating polyadenylation, but hnRNP H2 had a positive effect, whereas hnRNP F acted negatively. We therefore carried out side-by-side comparisons of their RNA-binding and in vivo actions. The binding of the CstF2 (64 kDa cleavage stimulatory factor) to SV40 (simian virus 40) late pre-mRNA substrates containing a downstream GRS (guanine-rich sequence) was reduced by hnRNP F, but not by hnRNP H2, in a UV-cross-linking assay. Point mutations of the 14-nt GRS influenced the binding of purified hnRNP F or H2 in parallel. Co-operative binding of the individual proteins to RNA was lost with mutations of the GRS in the G1-5 or G12-14 regions; both regions seem to be necessary for optimal interactions. Using a reporter green fluorescent protein assay with the GRS inserted downstream of the poly(A) (polyadenine) signal, expression in vivo was diminished by a mutant G1-5 sequence which decreased binding of both hnRNPs (SAA20) and was enhanced by a 12-14-nt mutant that showed enhanced hnRNP F or H2 binding (SAA10). Using small interfering RNA, down-regulation of hnRNP H2 levels diminished reporter expression, confirming that hnRNP H2 confers a positive influence; in contrast, decreasing hnRNP F levels had a negligible influence on reporter expression with the intact GRS. A pronounced diminution in reporter expression was seen with the SAA20 mutant for both. Thus the relative levels of hnRNP F and H2 in cells, as well as the target sequences in the downstream GRS on pre-mRNA, influence gene expression.
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Affiliation(s)
- Serkan A. Alkan
- *Program in Biochemistry and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A
- †Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A
| | - Kathleen Martincic
- †Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A
| | - Christine Milcarek
- †Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, U.S.A
- To whom correspondence should be addressed (email )
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40
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Pan Z, Zhang H, Hague LK, Lee JY, Lutz CS, Tian B. An intronic polyadenylation site in human and mouse CstF-77 genes suggests an evolutionarily conserved regulatory mechanism. Gene 2006; 366:325-34. [PMID: 16316725 DOI: 10.1016/j.gene.2005.09.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Revised: 08/09/2005] [Accepted: 09/22/2005] [Indexed: 01/24/2023]
Abstract
Human CstF-77 is one of the three subunits of cleavage stimulation factor (CstF) that is essential for mRNA polyadenylation. Its Drosophila homologue, suppressor of forked [su(f)], contains an intronic poly(A) site, which can lead to a short transcript without a stop codon. By both bioinformatic searches and validation with molecular biology experiments, we found that human and mouse CstF-77 genes also contain an intronic poly(A) site, which can be utilized to produce short CstF-77 transcripts lacking sequences encoding domains that are involved in many of the CstF-77 functions. The genomic sequence surrounding the poly(A) site is highly conserved among all vertebrates, but is not present in non-vertebrate species. Using public Serial Analysis of Gene Expression (SAGE) data, we found that the intronic poly(A) site is utilized in a wide range of tissues. This finding indicates that vertebrates may employ a similar alternative polyadenylation mechanism to modulate CstF-77, highlighting the importance of the regulation of CstF-77 in various species.
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Affiliation(s)
- Zhenhua Pan
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07101, USA
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41
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Li L, Roy K, Katyal S, Sun X, Bléoo S, Godbout R. Dynamic nature of cleavage bodies and their spatial relationship to DDX1 bodies, Cajal bodies, and gems. Mol Biol Cell 2005; 17:1126-40. [PMID: 16371507 PMCID: PMC1382303 DOI: 10.1091/mbc.e05-08-0768] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DDX1 bodies, cleavage bodies, Cajal bodies (CBs), and gems are nuclear suborganelles that contain factors involved in RNA transcription and/or processing. Although all four nuclear bodies can exist as distinct entities, they often colocalize or overlap with each other. To better understand the relationship between these four nuclear bodies, we examined their spatial distribution as a function of the cell cycle. Here, we report that whereas DDX1 bodies, CBs and gems are present throughout interphase, CPSF-100-containing cleavage bodies are predominantly found during S and G2 phases, whereas CstF-64-containing cleavage bodies are primarily observed during S phase. All four nuclear bodies associate with each other during S phase, with cleavage bodies colocalizing with DDX1 bodies, and cleavage bodies/DDX1 bodies residing adjacent to gems and CBs. Although inhibitors of RNA transcription had no effect on DDX1 bodies or cleavage bodies, inhibitors of DNA replication resulted in loss of CstF-64-containing cleavage bodies. A striking effect on nuclear structures was observed with latrunculin B, an inhibitor of actin polymerization, resulting in the formation of needlelike nuclear spicules made up of CstF-64, CPSF-100, RNA, and RNA polymerase II. Our results suggest that cleavage body components are highly dynamic in nature.
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Affiliation(s)
- Lei Li
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
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42
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Thomadaki H, Tsiapalis CM, Scorilas A. Polyadenylate polymerase modulations in human epithelioid cervix and breast cancer cell lines, treated with etoposide or cordycepin, follow cell cycle rather than apoptosis induction. Biol Chem 2005; 386:471-80. [PMID: 15927891 DOI: 10.1515/bc.2005.056] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Cancer results from an imbalance between cell cycle progression and apoptosis. Therefore, most anticancer drugs exert their antiproliferative and cytotoxic activity via cell cycle arrest and induction of apoptosis, a controlled form of cell death that is dysregulated in cancer. Many polyadenylation trans-acting factors, including polyadenylate polymerase (PAP), are increasingly found to be involved in cell cycle, apoptosis and cancer prognosis. The objective of the present study was to identify PAP modulations in the response of two epithelial cancer cell lines (HeLa and MCF-7) to apoptosis induction by the anticancer drugs etoposide and cordycepin. Cells were assessed for PAP activity and isoforms by the highly sensitive PAP activity assay and Western blotting, respectively. Induction of apoptosis was determined by endonucleosomal DNA cleavage, 4'6-diamidino-2-phenylindol (DAPI) staining and caspase-6 activity assay, whereas cytotoxicity and cell cycle status were assessed by trypan blue staining, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and flow cytometry. Our results indicate that PAP changes very early in response to either etoposide or cordycepin treatment, even prior to the hallmarks of apoptosis (chromatin condensation and cleavage), in both cell lines tested, but in a different mode. Our results suggest, for the first time, that in the epithelial cancer cell lines used, PAP modulations follow cell cycle progression rather than the course of apoptosis.
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Affiliation(s)
- Hellinida Thomadaki
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Athens, Panepistimiopolis, GR-15701 Athens, Greece
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43
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Kolev NG, Steitz JA. Symplekin and multiple other polyadenylation factors participate in 3'-end maturation of histone mRNAs. Genes Dev 2005; 19:2583-92. [PMID: 16230528 PMCID: PMC1276732 DOI: 10.1101/gad.1371105] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Most metazoan messenger RNAs encoding histones are cleaved, but not polyadenylated at their 3' ends. Processing in mammalian cell extracts requires the U7 small nuclear ribonucleoprotein (U7 snRNP) and an unidentified heat-labile factor (HLF). We describe the identification of a heat-sensitive protein complex whose integrity is required for histone pre-mRNA cleavage. It includes all five subunits of the cleavage and polyadenylation specificity factor (CPSF), two subunits of the cleavage stimulation factor (CstF), and symplekin. Reconstitution experiments reveal that symplekin, previously shown to be necessary for cytoplasmic poly(A) tail elongation and translational activation of mRNAs during Xenopus oocyte maturation, is the essential heat-labile component. Thus, a common molecular machinery contributes to the nuclear maturation of mRNAs both lacking and possessing poly(A), as well as to cytoplasmic poly(A) tail elongation.
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Affiliation(s)
- Nikolay G Kolev
- Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA
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44
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Shell SA, Hesse C, Morris SM, Milcarek C. Elevated levels of the 64-kDa cleavage stimulatory factor (CstF-64) in lipopolysaccharide-stimulated macrophages influence gene expression and induce alternative poly(A) site selection. J Biol Chem 2005; 280:39950-61. [PMID: 16207706 DOI: 10.1074/jbc.m508848200] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Lipopolysaccharide (LPS) activation of murine RAW 264.7 macrophages influences the expression of multiple genes through transcriptional and post-transcriptional mechanisms. We observed a 5-fold increase in CstF-64 expression following LPS treatment of RAW macrophages. The increase in CstF-64 protein was specific in that several other factors involved in 3'-end processing were not affected by LPS stimulation. Activation of RAW macrophages with LPS caused an increase in proximal poly(A) site selection within a reporter mini-gene containing two linked poly(A) sites that occurred concomitant with the increase in CstF-64 expression. Furthermore, forced overexpression of the CstF-64 protein also induced alternative poly(A) site selection on the reporter minigene. Microarray analysis performed on CstF-64 overexpressing RAW macrophages revealed that elevated levels of CstF-64 altered the expression of 51 genes, 14 of which showed similar changes in gene expression with LPS stimulation. Sequence analysis of the 3'-untranslated regions of these 51 genes revealed that over 45% possess multiple putative poly(A) sites. Two of these 51 genes demonstrated alternative polyadenylation under both LPS-stimulating and CstF-64-overexpressing conditions. We concluded that the physiologically increased levels of CstF-64 observed in LPS-stimulated RAW macrophages contribute to the changes in expression and alternative polyadenylation of a number of genes, thus identifying another level of gene regulation that occurs in macrophages activated with LPS.
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MESH Headings
- 3' Untranslated Regions
- Algorithms
- Animals
- Binding Sites
- Blotting, Western
- Cell Proliferation
- Cells, Cultured
- Cleavage Stimulation Factor/chemistry
- Cleavage Stimulation Factor/physiology
- Gene Expression Regulation
- Genes, Reporter
- Lipopolysaccharides/metabolism
- Lipopolysaccharides/pharmacology
- Macrophages/metabolism
- Mice
- Mice, Inbred C57BL
- Models, Biological
- Models, Genetic
- Models, Statistical
- Oligonucleotide Array Sequence Analysis
- Oligonucleotides/chemistry
- Open Reading Frames
- Poly A/chemistry
- Polyadenylation
- Promoter Regions, Genetic
- Protein Binding
- Protein Conformation
- RNA/chemistry
- RNA Processing, Post-Transcriptional
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Time Factors
- Transcription, Genetic
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Affiliation(s)
- Scott A Shell
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15221, USA
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45
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Wei CC, Guo DF, Zhang SL, Ingelfinger JR, Chan JSD. Heterogenous nuclear ribonucleoprotein F modulates angiotensinogen gene expression in rat kidney proximal tubular cells. J Am Soc Nephrol 2005; 16:616-28. [PMID: 15659559 DOI: 10.1681/asn.2004080715] [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: 11/03/2022] Open
Abstract
An insulin-responsive element (IRE) in the rat angiotensinogen (ANG) gene promoter that binds to two nuclear proteins with apparent molecular weights of 48 and 70 kD was identified previously from rat immortalized renal proximal tubular cells (IRPTC). The present studies aimed to identify and clone the 48-kD nuclear protein and to define its action on ANG gene expression. Nuclear proteins were isolated from IRPTC and subjected to two-dimensional electrophoresis. The 48-kD nuclear protein was detected by Southwestern blotting and subsequently identified by mass spectrometry, revealing that it was identical to 46-kD heterogeneous nuclear ribonucleoprotein F (hnRNP F), a nuclear protein that binds to TATA-binding protein and associates with RNA polymerase II and also interacts with nuclear cap-binding complex. The hnRNP F cDNA was cloned from IRPTC by reverse transcriptase-PCR. Bacterially expressed recombinant hnRNP F bound to the rat ANG-IRE, as revealed by gel mobility shift assay. The addition of polyclonal antibodies against hnRNP F yielded a supershift in gel mobility. Transient transfer of sense and antisense hnRNP F cDNA in IRPTC inhibited and enhanced ANG gene expression, respectively. High glucose stimulated and insulin inhibited hnRNP F expression in IRPTC. Expression studies indicated that hnRNP F is present in the kidney, testis, liver, lung, and brain but not in the spleen. In conclusion, these studies demonstrate that hnRNP F binds to rANG-IRE and modulates renal ANG gene expression, implicating that dysregulation of hnRNP F might affect renin-angiotensin system activation and, subsequently, kidney injury in diabetes.
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Affiliation(s)
- Chih-Chang Wei
- Centre de recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Hôtel-Dieu Pavillon Masson, 3850 Saint Urbain Street, Montreal, Quebec, Canada H2W 1T8
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46
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Sciammas R, Davis MM. Blimp-1; immunoglobulin secretion and the switch to plasma cells. Curr Top Microbiol Immunol 2005; 290:201-24. [PMID: 16480044 DOI: 10.1007/3-540-26363-2_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The transcription factor Blimp-1 governs the generation of plasma cells and immunoglobulin secretion. Recent microarray experiments indicate that Blimp-1 regulates a large set of genes that constitute a significant part of the plasma cell expression signature. The variety of differentially expressed genes indicates that Blimp-1 affects numerous aspects of plasma cell maturation, ranging from migration, adhesion, and homeostasis, to antibody secretion. In addition, Blimp-1 regulates immunoglobulin secretion by affecting the nuclear processing of the mRNA transcript and by affecting protein trafficking by regulating genes that impact on the activity of the endoplasmic reticulum. Interestingly, the differentiation events that Blimp-1 regulates appear to be modulated depending on the activation state of the B cell. This modulation may be due at least in part to distinct regions of Blimp-1 that regulate unique sets of genes independently of each other. These data hint at the complexity of Blimp-1 and the genetic program that it initiates to produce a pool of plasma cells necessary for specific immunity.
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Affiliation(s)
- R Sciammas
- Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637, USA.
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47
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Phillips C, Pachikara N, Gunderson SI. U1A inhibits cleavage at the immunoglobulin M heavy-chain secretory poly(A) site by binding between the two downstream GU-rich regions. Mol Cell Biol 2004; 24:6162-71. [PMID: 15226420 PMCID: PMC434241 DOI: 10.1128/mcb.24.14.6162-6171.2004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The immunoglobulin M heavy-chain locus contains two poly(A) sites which are alternatively expressed during B-cell differentiation. Despite its promoter proximal location, the secretory poly(A) site is not expressed in undifferentiated cells. Crucial to the activation of the secretory poly(A) site during B-cell differentiation are changes in the binding of cleavage stimulatory factor 64K to GU-rich elements downstream of the poly(A) site. What regulates this change is not understood. The secretory poly(A) site contains two downstream GU-rich regions separated by a 29-nucleotide sequence. Both GU-rich regions are necessary for binding of the specific cleavage-polyadenylation complex. We demonstrate here that U1A binds two (AUGCN(1-3)C) motifs within the 29-nucleotide sequence and inhibits the binding of cleavage stimulatory factor 64K and cleavage at the secretory poly(A) site.
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Affiliation(s)
- Catherine Phillips
- Molecular Biology and Biochemistry, Rutgers University, Nelson Labs, Room A322, 604 Allison Rd., Piscataway, NJ 08854, USA.
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48
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Sciammas R, Davis MM. Modular Nature of Blimp-1 in the Regulation of Gene Expression during B Cell Maturation. THE JOURNAL OF IMMUNOLOGY 2004; 172:5427-40. [PMID: 15100284 DOI: 10.4049/jimmunol.172.9.5427] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The transcription factor Blimp-1 induces the maturation of B cells into Ab-secreting plasma cells. DNA microarrays were used to analyze the transcription profiles of both Blimp-1-transduced murine B cell lines and the inducible B cell line BCL(1). Hundreds of genes were differentially regulated, showing how Blimp-1 both restricts affinity maturation and promotes Ab secretion, homeostasis, migration, and differentiation. Strikingly, when different modes of plasma cell induction are used, very different genetic programs are used, suggesting that the transition from a B cell to plasma cell can occur in multiple ways, perhaps accounting for the different types of Ab-secreting cells observed in vivo. Furthermore, mutagenesis of Blimp-1 reveals multiple effector domains, which regulate distinct genes. This indicates that Blimp-1 subdivides the maturation program into select and tunable pathways.
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Affiliation(s)
- Roger Sciammas
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Brown KM, Gilmartin GM. A mechanism for the regulation of pre-mRNA 3' processing by human cleavage factor Im. Mol Cell 2004; 12:1467-76. [PMID: 14690600 DOI: 10.1016/s1097-2765(03)00453-2] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Human cleavage factor I(m) (CFI(m)) is a heterodimeric RNA binding protein complex that functions at an early step in the assembly of the pre-mRNA 3' processing complex. In this report we show that CFI(m) can stimulate both cleavage and poly(A) addition, and can act to suppress poly(A) site cleavage in a sequence-dependent manner. Elevated levels of CFI(m) suppressed cleavage at the primary poly(A) site of the pre-mRNA encoding the 68 kDa subunit of CFI(m). CFI(m)-mediated suppression of poly(A) site cleavage was dependent upon the presence of three copies of an RNA element initially identified by CFI(m)-SELEX. These data provide evidence for a mechanism for the regulation of poly(A) site selection by a basal pre-mRNA 3' processing factor.
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Affiliation(s)
- Kirk M Brown
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
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50
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Wallace AM, Denison TL, Attaya EN, MacDonald CC. Developmental distribution of the polyadenylation protein CstF-64 and the variant tauCstF-64 in mouse and rat testis. Biol Reprod 2003; 70:1080-7. [PMID: 14681198 DOI: 10.1095/biolreprod.103.022947] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Messenger RNA polyadenylation is one of the processes that control gene expression in all eukaryotic cells and tissues. In mice, two forms of the regulatory polyadenylation protein CstF-64 are found. The gene Cstf2 on the X chromosome encodes this form, and it is expressed in all somatic tissues. The second form, tauCstF-64 (encoded by the autosomal gene Cstf2t), is expressed in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells and, to a smaller extent, in brain. We report here that whereas CstF-64 and tauCstF-64 expression in rat tissues resembles their expression in mouse tissues, significant differences also are found. First, unlike in mice, in which CstF-64 was expressed in postmeiotic round and elongating spermatids, rat CstF-64 was absent in those cell types. Second, unlike in mice, tauCstF-64 was expressed at significant levels in rat liver. These differences in expression suggest interesting differences in X-chromosomal gene expression between these two rodent species.
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Affiliation(s)
- A Michelle Wallace
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, USA
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