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Cao H. Lipopolysaccharide regulation of antiinflammatory tristetraprolin family and proinflammatory gene expression in mouse macrophages. BMC Res Notes 2024; 17:82. [PMID: 38504371 PMCID: PMC10949775 DOI: 10.1186/s13104-024-06743-6] [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: 09/26/2023] [Accepted: 03/08/2024] [Indexed: 03/21/2024] Open
Abstract
OBJECTIVE Tristetraprolin (TTP/ZFP36) family proteins exhibit antiinflammatory effects by destabilizing proinflammatory mRNAs. Previous studies showed that bacterial endotoxin lipopolysaccharides (LPS) stimulated TTP and tumor necrosis factor (TNF) gene expression, but less was known about LPS effects on TTP homologues and other proinflammatory gene expression in macrophages. The objective was to investigate LPS regulation of TTP family gene and TTP-targeted gene expression in mouse RAW264.7 macrophages using much higher concentrations of LPS and much longer treatment time than previous studies. RESULTS MTT assay showed that LPS was not toxic to the cells under LPS treatment up to 1000 ng/mL for 2-24 h. LPS mildly affected the soluble protein content in the cells. qPCR assay showed that LPS stimulated TTP mRNA rapidly but not sustainably with 40, 10, and 3 fold of the DMSO control after 2, 8 and 24 h treatment, respectively. Immunoblotting confirmed qPCR results on LPS stimulation of TTP gene expression in the mouse macrophages. LPS exhibited minimal effects on ZFP36L1, ZFP36L2 and ZFP36L3 mRNA levels. LPS increased mRNA levels of TNF, COX2, GM-CSF, INFγ and IL12b up to 311, 418, 11, 9 and 4 fold, respectively. This study demonstrated that LPS did not affect macrophage viability, dramatically increased antiinflammatory TTP gene expression as well as proinflammatory TNF and COX2 gene expression but had only mild effects on TTP homologues and other proinflammatory cytokine gene expression in the mouse macrophages.
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Affiliation(s)
- Heping Cao
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, 1100 Allen Toussaint Blvd, New Orleans, LA, 70124, USA.
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2
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Zhang Q, Zhang Y, Jing L, Zhao H. Microplastics induced inflammation in the spleen of developmental Japanese quail (Coturnix japonica) via ROS-mediated p38 MAPK and TNF signaling pathway activation 1. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 341:122891. [PMID: 37951530 DOI: 10.1016/j.envpol.2023.122891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/19/2023] [Accepted: 11/05/2023] [Indexed: 11/14/2023]
Abstract
Microplastics (MPs) have been found in virtually every environment on earth and become a source of pollution around the world. The toxicology of microplastics on immunity is an emerging area of research, and more studies are needed to fully understand the effects of microplastics exposure on animal health. Therefore, we tried to determine the immunotoxic effects of microplastics on avian spleen by using an animal model- Japanese quail (Coturnix japonica). One-week chicks were exposed to environmentally relevant concentrations of 0.02 mg/kg, 0.4 mg/kg and 8 mg/kg polystyrene microplastics in the feed for 5 weeks. The results demonstrated that microplastics induced microstructural injuries featured by cell disarrangement and vacuolation indicating splenic inflammation. Ultrastructural damages including membrane lysis and mitochondrial vacuolation also suggested inflammatory responses in the spleen by microplastics exposure. Meanwhile, increasing reactive oxygen species (ROS) and Malondialdehyde (MDA) while the inactivation of superoxide dismutase (SOD), catalase (CAT) and glutathione S-transferase (GST) indicated oxidative stress in the spleen. Moreover, the increasing level of proinflammatory cytokines including Tumor necrosis factor alpha (TNF-α), interferon gamma (IFN-γ), interleukin-1β (IL-1β), interleukin-6 (IL-6) and decreasing level of anti-inflammatory cytokine interleukin-10 (IL-10) implied splenic inflammation. Furthermore, transcriptomic analysis showed that microplastics induced inflammatory responses in the spleen through p38 mitogen-activated protein kinases (p38 MAPK) pathway activation and tumor necrosis factor (TNF) signaling stimulation. The signaling stimulation also aggravated cell apoptosis in the spleen. The present study may benefit to understand potential mechanisms of developmental immunotoxicology of microplastics.
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Affiliation(s)
- Qingyu Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yuxin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Lingyang Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Hongfeng Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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Snyder BL, Huang R, Burkholder AB, Donahue DR, Mahler BW, Bortner CD, Lai WS, Blackshear PJ. Synergistic roles of tristetraprolin family members in myeloid cells in the control of inflammation. Life Sci Alliance 2024; 7:e202302222. [PMID: 37903626 PMCID: PMC10616675 DOI: 10.26508/lsa.202302222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
Members of the tristetraprolin (TTP) family of RNA-binding proteins can bind to and promote the decay of specific transcripts containing AU-rich motifs. ZFP36 (TTP) is best known for regulating pro-inflammatory cytokine expression in myeloid cells; however, its mammalian paralogues ZFP36L1 and ZFP36L2 have not been viewed as important in controlling inflammation. We knocked out these genes in myeloid cells in mice, singly and together. Single-gene myeloid-specific knockouts resulted in almost no spontaneous phenotypes. In contrast, mice with myeloid cell deficiency of all three genes developed severe inflammation, with a median survival of 8 wk. Macrophages from these mice expressed many more stabilized transcripts than cells from myeloid-specific TTP knockout mice; many of these encoded pro-inflammatory cytokines and chemokines. The failure of weight gain, arthritis, and early death could be prevented completely by two normal alleles of any of the three paralogues, and even one normal allele of Zfp36 or Zfp36l2 was enough to prevent the inflammatory phenotype. Our findings emphasize the importance of all three family members, acting in concert, in myeloid cell function.
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Affiliation(s)
- Brittany L Snyder
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Rui Huang
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Adam B Burkholder
- https://ror.org/01cwqze88 Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Danielle R Donahue
- NIH Mouse Imaging Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Beth W Mahler
- Experimental Pathology Laboratories, Inc., Research Triangle Park, Durham, NC, USA
| | - Carl D Bortner
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Wi S Lai
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
| | - Perry J Blackshear
- https://ror.org/01cwqze88 Signal Transduction Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, USA
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
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Guth S, Mollentze N, Renault K, Streicker DG, Visher E, Boots M, Brook CE. Bats host the most virulent-but not the most dangerous-zoonotic viruses. Proc Natl Acad Sci U S A 2022; 119:e2113628119. [PMID: 35349342 DOI: 10.1101/2021.07.25.453574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
SignificanceThe clear need to mitigate zoonotic risk has fueled increased viral discovery in specific reservoir host taxa. We show that a combination of viral and reservoir traits can predict zoonotic virus virulence and transmissibility in humans, supporting the hypothesis that bats harbor exceptionally virulent zoonoses. However, pandemic prevention requires thinking beyond zoonotic capacity, virulence, and transmissibility to consider collective "burden" on human health. For this, viral discovery targeting specific reservoirs may be inefficient as death burden correlates with viral, not reservoir, traits, and depends on context-specific epidemiological dynamics across and beyond the human-animal interface. These findings suggest that longitudinal studies of viral dynamics in reservoir and spillover host populations may offer the most effective strategy for mitigating zoonotic risk.
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Affiliation(s)
- Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Nardus Mollentze
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Katia Renault
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Daniel G Streicker
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Elisa Visher
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
- Centre for Ecology and Conservation, University of Exeter, Exeter TR10 9FE, United Kingdom
| | - Cara E Brook
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
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Guth S, Mollentze N, Renault K, Streicker DG, Visher E, Boots M, Brook CE. Bats host the most virulent-but not the most dangerous-zoonotic viruses. Proc Natl Acad Sci U S A 2022; 119:e2113628119. [PMID: 35349342 PMCID: PMC9168486 DOI: 10.1073/pnas.2113628119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/09/2022] [Indexed: 01/06/2023] Open
Abstract
SignificanceThe clear need to mitigate zoonotic risk has fueled increased viral discovery in specific reservoir host taxa. We show that a combination of viral and reservoir traits can predict zoonotic virus virulence and transmissibility in humans, supporting the hypothesis that bats harbor exceptionally virulent zoonoses. However, pandemic prevention requires thinking beyond zoonotic capacity, virulence, and transmissibility to consider collective "burden" on human health. For this, viral discovery targeting specific reservoirs may be inefficient as death burden correlates with viral, not reservoir, traits, and depends on context-specific epidemiological dynamics across and beyond the human-animal interface. These findings suggest that longitudinal studies of viral dynamics in reservoir and spillover host populations may offer the most effective strategy for mitigating zoonotic risk.
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Affiliation(s)
- Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Nardus Mollentze
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Katia Renault
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Daniel G. Streicker
- Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Elisa Visher
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
- Centre for Ecology and Conservation, University of Exeter, Exeter TR10 9FE, United Kingdom
| | - Cara E. Brook
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
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Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation. iScience 2022; 25:103899. [PMID: 35243257 PMCID: PMC8873613 DOI: 10.1016/j.isci.2022.103899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/12/2021] [Accepted: 02/07/2022] [Indexed: 11/20/2022] Open
Abstract
The phenotypic plasticity in responses to short-term stress can provide clues for understanding the adaptive fixation mechanism of genetic variation during long-term exposure to extreme environments. However, few studies have compared short-term stress responses with long-term evolutionary patterns; in particular, no interactions between the two processes have been evaluated in high-altitude environment. We performed RNA sequencing in embryo fibroblasts derived from great tits and mice to explore transcriptional responses after exposure to simulated high-altitude environmental stresses. Transcriptional changes of genes associated with metabolic pathways were identified in both bird and mice cells after short-term stress responses. Genomic comparisons among long-term highland tits and mammals and their lowland relatives revealed similar pathways (e.g., metabolic pathways) with that initiated under short-term stress transcriptional responses in vitro. These findings highlight the indicative roles of short-term stress in the long-term adaptation, and adopt common paths to molecular adaptation in mouse and bird cells. Short-term stress and long-term adaptations share the common metabolic pathways Phenotypic plasticity can promote adaptive evolution Adopt common paths to molecular adaptation in mouse and bird cells
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7
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Thachil J. Hemostasis in tweeters. J Thromb Haemost 2022; 20:272-273. [PMID: 34954883 DOI: 10.1111/jth.15594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Jecko Thachil
- Department of Haematology, Manchester University Hospitals, Manchester, UK
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The Tristetraprolin Family of RNA-Binding Proteins in Cancer: Progress and Future Prospects. Cancers (Basel) 2020; 12:cancers12061539. [PMID: 32545247 PMCID: PMC7352335 DOI: 10.3390/cancers12061539] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Post-transcriptional regulation of gene expression plays a key role in cellular proliferation, differentiation, migration, and apoptosis. Increasing evidence suggests dysregulated post-transcriptional gene expression as an important mechanism in the pathogenesis of cancer. The tristetraprolin family of RNA-binding proteins (RBPs), which include Zinc Finger Protein 36 (ZFP36; commonly referred to as tristetraprolin (TTP)), Zinc Finger Protein 36 like 1 (ZFP36L1), and Zinc Finger Protein 36 like 2 (ZFP36L2), play key roles in the post-transcriptional regulation of gene expression. Mechanistically, these proteins function by binding to the AU-rich elements within the 3′-untranslated regions of their target mRNAs and, in turn, increasing mRNA turnover. The TTP family RBPs are emerging as key regulators of multiple biological processes relevant to cancer and are aberrantly expressed in numerous human cancers. The TTP family RBPs have tumor-suppressive properties and are also associated with cancer prognosis, metastasis, and resistance to chemotherapy. Herein, we summarize the various hallmark molecular traits of cancers that are reported to be regulated by the TTP family RBPs. We emphasize the role of the TTP family RBPs in the regulation of trait-associated mRNA targets in relevant cancer types/cell lines. Finally, we highlight the potential of the TTP family RBPs as prognostic indicators and discuss the possibility of targeting these TTP family RBPs for therapeutic benefits.
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Avian Bornaviral Ganglioneuritis: Current Debates and Unanswered Questions. Vet Med Int 2020; 2020:6563723. [PMID: 32411340 PMCID: PMC7212328 DOI: 10.1155/2020/6563723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/03/2020] [Indexed: 12/15/2022] Open
Abstract
Avian bornaviral ganglioneuritis, often referred to as parrot wasting disease, is associated with a newly discovered avian virus from the taxonomic family Bornaviridae. Research regarding the pathogenesis and treatment for this disease is ongoing, with implications for understanding other emerging human and nonhuman diseases, as well as the health and ecology of wildlife. At this time, numerous questions remain unanswered regarding the transmission of the disease, best practices for diagnostic sampling and testing, and whether currently used drug therapies are effective or harmful for afflicted birds. The pathogenesis of the disease also remains unclear with many birds showing resistance to the effects of the virus and being able to remain clinically unaffected for years, while other birds succumb to its effects. New research findings regarding avian bornaviral ganglioneuritis are discussed and important as yet unanswered questions are identified.
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Lai WS, Wells ML, Perera L, Blackshear PJ. The tandem zinc finger RNA binding domain of members of the tristetraprolin protein family. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1531. [PMID: 30864256 DOI: 10.1002/wrna.1531] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/12/2019] [Accepted: 02/20/2019] [Indexed: 12/23/2022]
Abstract
Tristetraprolin (TTP), the prototype member of the protein family of the same name, was originally discovered as the product of a rapidly inducible gene in mouse cells. Development of a knockout (KO) mouse established that absence of the protein led to a severe inflammatory syndrome, due in part to elevated levels of tumor necrosis factor (TNF). TTP was found to bind directly and with high affinity to specific AU-rich sequences in the 3'-untranslated region of the TNF mRNA. This initial binding led to promotion of TNF mRNA decay and inhibition of its translation. Many additional TTP target mRNAs have since been identified, some of which are cytokines and chemokines involved in the inflammatory response. There are three other proteins in the mouse with similar activities and domain structures, but whose KO phenotypes are remarkably different. Moreover, proteins with similar domain structures and activities have been found throughout eukaryotes, demonstrating that this protein family arose from an ancient ancestor. The defining characteristic of this protein family is the tandem zinc finger (TZF) domain, a 64 amino acid sequence with many conserved residues that is responsible for the direct RNA binding. We discuss here many aspects of this protein domain that have been elucidated since the original discovery of TTP, including its sequence conservation throughout eukarya; its apparent continued evolution in some lineages; its functional dependence on many key conserved residues; its "interchangeability" among evolutionarily distant species; and the evidence that RNA binding is required for the physiological functions of the proteins. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Wi S Lai
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Melissa L Wells
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina.,Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina
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Lai WS, Arvola RM, Goldstrohm AC, Blackshear PJ. Inhibiting transcription in cultured metazoan cells with actinomycin D to monitor mRNA turnover. Methods 2019; 155:77-87. [PMID: 30625384 DOI: 10.1016/j.ymeth.2019.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 12/11/2022] Open
Abstract
Decay of transcribed mRNA is a key determinant of steady state mRNA levels in cells. Global analysis of mRNA decay in cultured cells has revealed amazing heterogeneity in rates of decay under normal growth conditions, with calculated half-lives ranging from several minutes to many days. The factors that are responsible for this wide range of decay rates are largely unknown, although our knowledge of trans-acting RNA binding proteins and non-coding RNAs that can control decay rates is increasing. Many methods have been used to try to determine mRNA decay rates under various experimental conditions in cultured cells, and transcription inhibitors like actinomycin D have probably the longest history of any technique for this purpose. Despite this long history of use, the actinomycin D method has been criticized as prone to artifacts, and as ineffective for some promoters. With appropriate guidelines and controls, however, it can be a versatile, effective technique for measuring endogenous mRNA decay in cultured mammalian and insect cells, as well as the decay of exogenously-expressed transcripts. It can be used readily on a genome-wide level, and is remarkably cost-effective. In this short review, we will discuss our utilization of this approach in these cells; we hope that these methods will allow more investigators to apply this useful technique to study mRNA decay under the appropriate conditions.
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Affiliation(s)
- Wi S Lai
- The Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States
| | - Rene M Arvola
- The Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Aaron C Goldstrohm
- The Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Perry J Blackshear
- The Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States; The Departments of Medicine and Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States.
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Bassano I, Ong SH, Lawless N, Whitehead T, Fife M, Kellam P. Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes. BMC Genomics 2017; 18:419. [PMID: 28558694 PMCID: PMC5450142 DOI: 10.1186/s12864-017-3801-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/16/2017] [Indexed: 01/16/2023] Open
Abstract
Background Interferon inducible transmembrane (IFITM) proteins are effectors of the immune system widely characterized for their role in restricting infection by diverse enveloped and non-enveloped viruses. The chicken IFITM (chIFITM) genes are clustered on chromosome 5 and to date four genes have been annotated, namely chIFITM1, chIFITM3, chIFITM5 and chIFITM10. However, due to poor assembly of this locus in the Gallus Gallus v4 genome, accurate characterization has so far proven problematic. Recently, a new chicken reference genome assembly Gallus Gallus v5 was generated using Sanger, 454, Illumina and PacBio sequencing technologies identifying considerable differences in the chIFITM locus over the previous genome releases. Methods We re-sequenced the locus using both Illumina MiSeq and PacBio RS II sequencing technologies and we mapped RNA-seq data from the European Nucleotide Archive (ENA) to this finalized chIFITM locus. Using SureSelect probes capture probes designed to the finalized chIFITM locus, we sequenced the locus of a different chicken breed, namely a White Leghorn, and a turkey. Results We confirmed the Gallus Gallus v5 consensus except for two insertions of 5 and 1 base pair within the chIFITM3 and B4GALNT4 genes, respectively, and a single base pair deletion within the B4GALNT4 gene. The pull down revealed a single amino acid substitution of A63V in the CIL domain of IFITM2 compared to Red Jungle fowl and 13, 13 and 11 differences between IFITM1, 2 and 3 of chickens and turkeys, respectively. RNA-seq shows chIFITM2 and chIFITM3 expression in numerous tissue types of different chicken breeds and avian cell lines, while the expression of the putative chIFITM1 is limited to the testis, caecum and ileum tissues. Conclusions Locus resequencing using these capture probes and RNA-seq based expression analysis will allow the further characterization of genetic diversity within Galliformes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3801-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Bassano
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Division of Infectious Diseases, Department of Medicine, Imperial College Faculty of Medicine, Wright Fleming Wing, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Swee Hoe Ong
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nathan Lawless
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, GU24 0NF, UK
| | - Thomas Whitehead
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, GU24 0NF, UK
| | - Mark Fife
- The Pirbright Institute, Pirbright Laboratory, Ash Road, Woking, GU24 0NF, UK
| | - Paul Kellam
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Division of Infectious Diseases, Department of Medicine, Imperial College Faculty of Medicine, Wright Fleming Wing, St Mary's Campus, Norfolk Place, London, W2 1PG, UK.
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Wells ML, Perera L, Blackshear PJ. An Ancient Family of RNA-Binding Proteins: Still Important! Trends Biochem Sci 2017; 42:285-296. [PMID: 28096055 DOI: 10.1016/j.tibs.2016.12.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
Abstract
RNA-binding proteins are important modulators of mRNA stability, a crucial process that determines the ultimate cellular levels of mRNAs and their encoded proteins. The tristetraprolin (TTP) family of RNA-binding proteins appeared early in the evolution of eukaryotes, and has persisted in modern eukaryotes. The domain structures and biochemical functions of family members from widely divergent lineages are remarkably similar, but their mRNA 'targets' can be very different, even in closely related species. Recent gene knockout studies in species as distantly related as plants, flies, yeasts, and mice have demonstrated crucial roles for these proteins in a wide variety of physiological processes. Inflammatory and hematopoietic phenotypes in mice have suggested potential therapeutic approaches for analogous human disorders.
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Affiliation(s)
- Melissa L Wells
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA; Departments of Biochemistry and Medicine, Duke University Medical Center, Durham, NC 27710, USA.
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Das S, Sutoh Y, Hirano M, Han Q, Li J, Cooper MD, Herrin BR. Characterization of Lamprey BAFF-like Gene: Evolutionary Implications. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2016; 197:2695-703. [PMID: 27543613 PMCID: PMC5026938 DOI: 10.4049/jimmunol.1600799] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/25/2016] [Indexed: 12/25/2022]
Abstract
BAFF (TNF superfamily [TNFSF] 13B/Blys) and APRIL (TNFSF13) are important regulatory factors for lymphocyte activation and survival in mammals. A BAFF/APRIL-like relative called BAFF- and APRIL-like molecule (BALM) has also been identified in cartilaginous and bony fishes, and we report in this study a BAFF-like gene in lampreys. Our phylogenetic analysis of these genes and a related TNFSF12 gene called TNF-like weak inducer of apoptosis (TWEAK) suggest that, whereas an ancestral homolog of BAFF and APRIL was already present in a common ancestor of jawed and jawless vertebrates, TWEAK evolved early on in the jawed vertebrate lineage. Like mammalian BAFF and APRIL, the lamprey BAFF-like gene is expressed in T-like, B-like, and innate immune cells. The predicted protein encoded by this BAFF-like gene in lampreys exhibits higher sequence similarity with mammalian BAFF than APRIL. Correspondingly, we find BAFF orthologs in all of the jawed vertebrate representatives that we examined, although APRIL and/or BALM orthologs are not identifiable in certain jawed vertebrates. For example, BALM is not identifiable in tetrapods, and APRIL is not identifiable in several bony fishes or in birds, the latter of which also lack a TWEAK-like gene. Our analysis further suggests that a hybrid molecule called TWE-PRIL, which is a product of an in-genomic fusion between APRIL and TWEAK genes evolved early in mammalian evolution.
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Affiliation(s)
- Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, Atlanta, GA 30322
| | - Yoichi Sutoh
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, Atlanta, GA 30322
| | - Masayuki Hirano
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, Atlanta, GA 30322
| | - Qifeng Han
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, Atlanta, GA 30322
| | - Jianxu Li
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, Atlanta, GA 30322
| | - Max D Cooper
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, Atlanta, GA 30322
| | - Brantley R Herrin
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, Atlanta, GA 30322
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15
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Tristetraprolin as a Therapeutic Target in Inflammatory Disease. Trends Pharmacol Sci 2016; 37:811-821. [PMID: 27503556 DOI: 10.1016/j.tips.2016.07.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 11/22/2022]
Abstract
Members of the tristetraprolin (TTP) family of RNA-binding proteins are found in all major eukaryotic groups. TTP family members, from plants through humans, can bind adenosine-uridine rich elements in target mRNAs with high affinity. In mammalian cells, these proteins then promote deadenylation and decay of target transcripts. Four such proteins are found in mice, of which the best studied is TTP. When the gene encoding TTP is disrupted in mice, the animals develop a severe syndrome of arthritis, autoimmunity, cachexia, dermatitis, and myeloid hyperplasia. Conversely, recent overexpression studies have demonstrated protection against several experimental models of immune inflammatory disease. This endogenous anti-inflammatory protein could serve as the basis for novel approaches to therapy of similar conditions in humans.
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16
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Effects of Combined Tristetraprolin/Tumor Necrosis Factor Receptor Deficiency on the Splenic Transcriptome. Mol Cell Biol 2016; 36:1395-411. [PMID: 26976640 DOI: 10.1128/mcb.01068-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/23/2016] [Indexed: 12/15/2022] Open
Abstract
Tristetraprolin (TTP) acts by binding to AU-rich elements in certain mRNAs, such as tumor necrosis factor (TNF) mRNA, and increasing their decay rates. TTP knockout mice exhibit a profound inflammatory syndrome that is largely due to increased TNF levels. Although TTP's effects on gene expression have been well studied in cultured cells, little is known about its functions in intact tissues. We performed deep RNA sequencing on spleens from TTP knockout mice that were also deficient in both TNF receptors ("triple knockout" mice) to remove the secondary effects of excess TNF activity. To help identify posttranscriptionally regulated transcripts, we also compared changes in mature mRNA levels to levels of transiently expressed pre-mRNA. In the triple knockout spleens, levels of 3,014 transcripts were significantly affected by 1.5-fold or more, but only a small fraction exhibited differential mRNA/pre-mRNA changes suggestive of increased mRNA stability. Transferrin receptor mRNA, which contains two highly conserved potential TTP binding sites, was significantly upregulated relative to its pre-mRNA. This was reflected in increased transferrin receptor expression and increased splenic iron/hemosiderin deposition. Our results suggest that TTP deficiency has profound effects on the splenic transcriptome, even in the absence of secondary increases in TNF activity.
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17
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Gingerich TJ, Stumpo DJ, Lai WS, Randall TA, Steppan SJ, Blackshear PJ. Emergence and evolution of Zfp36l3. Mol Phylogenet Evol 2015; 94:518-530. [PMID: 26493225 DOI: 10.1016/j.ympev.2015.10.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/06/2015] [Accepted: 10/13/2015] [Indexed: 11/19/2022]
Abstract
In most mammals, the Zfp36 gene family consists of three conserved members, with a fourth member, Zfp36l3, present only in rodents. The ZFP36 proteins regulate post-transcriptional gene expression at the level of mRNA stability in organisms from humans to yeasts, and appear to be expressed in all major groups of eukaryotes. In Mus musculus, Zfp36l3 expression is limited to the placenta and yolk sac, and is important for overall fecundity. We sequenced the Zfp36l3 gene from more than 20 representative species, from members of the Muridae, Cricetidae and Nesomyidae families. Zfp36l3 was not present in Dipodidae, or any families that branched earlier, indicating that this gene is exclusive to the Muroidea superfamily. We provide evidence that Zfp36l3 arose by retrotransposition of an mRNA encoded by a related gene, Zfp36l2 into an ancestral rodent X chromosome. Zfp36l3 has evolved rapidly since its origin, and numerous modifications have developed, including variations in start codon utilization, de novo intron formation by mechanisms including a nested retrotransposition, and the insertion of distinct repetitive regions. One of these repeat regions, a long alanine rich-sequence, is responsible for the full-time cytoplasmic localization of Mus musculus ZFP36L3. In contrast, this repeat sequence is lacking in Peromyscus maniculatus ZFP36L3, and this protein contains a novel nuclear export sequence that controls shuttling between the nucleus and cytosol. Zfp36l3 is an example of a recently acquired, rapidly evolving gene, and its various orthologues illustrate several different mechanisms by which new genes emerge and evolve.
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Affiliation(s)
- Timothy J Gingerich
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Deborah J Stumpo
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Wi S Lai
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Thomas A Randall
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Scott J Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Perry J Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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18
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Newman R, McHugh J, Turner M. RNA binding proteins as regulators of immune cell biology. Clin Exp Immunol 2015. [PMID: 26201441 DOI: 10.1111/cei.12684] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific RNA binding proteins (RBP) are important regulators of the immune response. RBP modulate gene expression by regulating splicing, polyadenylation, localization, translation and decay of target mRNAs. Increasing evidence suggests that RBP play critical roles in the development, activation and function of lymphocyte populations in the immune system. This review will discuss the post-transcriptional regulation of gene expression by RBP during lymphocyte development, with particular focus on the Tristetraprolin family of RBP.
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Affiliation(s)
- R Newman
- Babraham Institute, Cambridge, UK
| | - J McHugh
- Babraham Institute, Cambridge, UK
| | - M Turner
- Babraham Institute, Cambridge, UK
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Neelamraju Y, Hashemikhabir S, Janga SC. The human RBPome: from genes and proteins to human disease. J Proteomics 2015; 127:61-70. [PMID: 25982388 DOI: 10.1016/j.jprot.2015.04.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/07/2015] [Accepted: 04/28/2015] [Indexed: 12/29/2022]
Abstract
RNA binding proteins (RBPs) play a central role in mediating post transcriptional regulation of genes. However less is understood about them and their regulatory mechanisms. In this study, we construct a catalogue of 1344 experimentally confirmed RBPs. The domain architecture of RBPs enabled us to classify them into three groups - Classical (29%), Non-classical (19%) and unclassified (52%). A higher percentage of proteins with unclassified domains reveals the presence of various uncharacterised motifs that can potentially bind RNA. RBPs were found to be highly disordered compared to Non-RBPs (p<2.2e-16, Fisher's exact test), suggestive of a dynamic regulatory role of RBPs in cellular signalling and homeostasis. Evolutionary analysis in 62 different species showed that RBPs are highly conserved compared to Non-RBPs (p<2.2e-16, Wilcox-test), reflecting the conservation of various biological processes like mRNA splicing and ribosome biogenesis. The expression patterns of RBPs from human proteome map revealed that ~40% of them are ubiquitously expressed and ~60% are tissue-specific. RBPs were also seen to be highly associated with several neurological disorders, cancer and inflammatory diseases. Anatomical contexts like B cells, T-cells, foetal liver and foetal brain were found to be strongly enriched for RBPs, implying a prominent role of RBPs in immune responses and different developmental stages. The catalogue and meta-analysis presented here should form a foundation for furthering our understanding of RBPs and the cellular networks they control, in years to come. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Yaseswini Neelamraju
- Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Seyedsasan Hashemikhabir
- Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Sarath Chandra Janga
- Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, United States.
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20
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Blackshear PJ, Perera L. Phylogenetic distribution and evolution of the linked RNA-binding and NOT1-binding domains in the tristetraprolin family of tandem CCCH zinc finger proteins. J Interferon Cytokine Res 2015; 34:297-306. [PMID: 24697206 DOI: 10.1089/jir.2013.0150] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In humans, the tristetraprolin or TTP family of CCCH tandem zinc finger (TZF) proteins comprises 3 members, encoded by the genes ZFP36, ZFP36L1, and ZFP36L2. These proteins have direct orthologues in essentially all vertebrates studied, with the exception of birds, which appear to lack a version of ZFP36. Additional family members are found in rodents, amphibians, and fish. In general, the encoded proteins contain 2 critical macromolecular interaction domains: the CCCH TZF domain, which is necessary for high-affinity binding to AU-rich elements in mRNA; and an extreme C-terminal domain that, in the case of TTP, interacts with NOT1, the scaffold of a large multi-protein complex that contains deadenylases. TTP and its related proteins act by first binding to AU-rich elements in mRNA, and then recruiting deadenylases to the mRNA, where they can processively remove the adenosine residues from the poly(A) tail. Highly conserved TZF domains have been found in unicellular eukaryotes such as yeasts, and these domains can bind AU-rich elements that resemble those bound by the mammalian proteins. However, certain fungi appear to lack proteins with intact TZF domains, and the TTP family proteins that are expressed in other fungi often lack the characteristic C-terminal NOT1 binding domain found in the mammalian proteins. For these reasons, we investigated the phylogenetic distribution of the relevant sequences in available databases. Both domains are present in family member proteins from most lineages of eukaryotes, suggesting their mutual presence in a common ancestor. However, the vertebrate type of NOT1-binding domain is missing in most fungi, and the TZF domain itself has disappeared or degenerated in recently evolved fungi. Nonetheless, both domains are present together in the proteins from several unicellular eukaryotes, including at least 1 fungus, and they seem to have remained together during the evolution of metazoans.
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Affiliation(s)
- Perry J Blackshear
- 1 Laboratories of Signal Transduction, National Institute of Environmental Health Sciences , Research Triangle Park, North Carolina
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Choi YJ, Lai WS, Fedic R, Stumpo DJ, Huang W, Li L, Perera L, Brewer BY, Wilson GM, Mason JM, Blackshear PJ. The Drosophila Tis11 protein and its effects on mRNA expression in flies. J Biol Chem 2014; 289:35042-60. [PMID: 25342740 DOI: 10.1074/jbc.m114.593491] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the mammalian tristetraprolin family of CCCH tandem zinc finger proteins can bind to certain AU-rich elements (AREs) in mRNAs, leading to their deadenylation and destabilization. Mammals express three or four members of this family, but Drosophila melanogaster and other insects appear to contain a single gene, Tis11. We found that recombinant Drosophila Tis11 protein could bind to ARE-containing RNA oligonucleotides with low nanomolar affinity. Remarkably, co-expression in mammalian cells with "target" RNAs demonstrated that Tis11 could promote destabilization of ARE-containing mRNAs and that this was partially dependent on a conserved C-terminal sequence resembling the mammalian NOT1 binding domain. Drosophila Tis11 promoted both deadenylation and decay of a target transcript in this heterologous cell system. We used chromosome deletion/duplication and P element insertion to produce two types of Tis11 deficiency in adult flies, both of which were viable and fertile. To address the hypothesis that Tis11 deficiency would lead to the abnormal accumulation of potential target transcripts, we analyzed gene expression in adult flies by deep mRNA sequencing. We identified 69 transcripts from 56 genes that were significantly up-regulated more than 1.5-fold in both types of Tis11-deficient flies. Ten of the up-regulated transcripts encoded probable proteases, but many other functional classes of proteins were represented. Many of the up-regulated transcripts contained potential binding sites for tristetraprolin family member proteins that were conserved in other Drosophila species. Tis11 is thus an ARE-binding, mRNA-destabilizing protein that may play a role in post-transcriptional gene expression in Drosophila and other insects.
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Affiliation(s)
| | - Wi S Lai
- From the Laboratories of Signal Transduction
| | | | | | | | | | - Lalith Perera
- Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Brandy Y Brewer
- the Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland 21201, and
| | - Gerald M Wilson
- the Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland 21201, and
| | | | - Perry J Blackshear
- From the Laboratories of Signal Transduction, the Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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