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Cackett G, Matelska D, Sýkora M, Portugal R, Malecki M, Bähler J, Dixon L, Werner F. The African Swine Fever Virus Transcriptome. J Virol 2020; 94:e00119-20. [PMID: 32075923 PMCID: PMC7163114 DOI: 10.1128/jvi.00119-20] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 02/04/2020] [Indexed: 11/20/2022] Open
Abstract
African swine fever virus (ASFV) causes hemorrhagic fever in domestic pigs, presenting the biggest global threat to animal farming in recorded history. Despite the importance of ASFV, little is known about the mechanisms and regulation of ASFV transcription. Using RNA sequencing methods, we have determined total RNA abundance, transcription start sites, and transcription termination sites at single-nucleotide resolution. This allowed us to characterize DNA consensus motifs of early and late ASFV core promoters, as well as a polythymidylate sequence determinant for transcription termination. Our results demonstrate that ASFV utilizes alternative transcription start sites between early and late stages of infection and that ASFV RNA polymerase (RNAP) undergoes promoter-proximal transcript slippage at 5' ends of transcription units, adding quasitemplated AU- and AUAU-5' extensions to mRNAs. Here, we present the first much-needed genome-wide transcriptome study that provides unique insight into ASFV transcription and serves as a resource to aid future functional analyses of ASFV genes which are essential to combat this devastating disease.IMPORTANCE African swine fever virus (ASFV) causes incurable and often lethal hemorrhagic fever in domestic pigs. In 2020, ASF presents an acute and global animal health emergency that has the potential to devastate entire national economies as effective vaccines or antiviral drugs are not currently available (according to the Food and Agriculture Organization of the United Nations). With major outbreaks ongoing in Eastern Europe and Asia, urgent action is needed to advance our knowledge about the fundamental biology of ASFV, including the mechanisms and temporal control of gene expression. A thorough understanding of RNAP and transcription factor function, and of the sequence context of their promoter motifs, as well as accurate knowledge of which genes are expressed when and the amino acid sequence of the encoded proteins, is direly needed for the development of antiviral drugs and vaccines.
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Affiliation(s)
- Gwenny Cackett
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | - Dorota Matelska
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
| | - Michal Sýkora
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czechia
| | | | - Michal Malecki
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Jürg Bähler
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Linda Dixon
- Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Finn Werner
- Institute for Structural and Molecular Biology, University College London, London, United Kingdom
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Liu H, Sun Q, Zhang M, Zhang Z, Fan X, Yuan H, Li C, Guo Y, Ning W, Sun Y, Song Y, Yu C. Differential expression of folate receptor 1 in medulloblastoma and the correlation with clinicopathological characters and target therapeutic potential. Oncotarget 2018; 8:23048-23060. [PMID: 28416738 PMCID: PMC5410284 DOI: 10.18632/oncotarget.15480] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/07/2017] [Indexed: 12/18/2022] Open
Abstract
Medulloblastoma is the most common malignant brain tumor in children. Folate receptor 1 (Folr1) was abundantly expressed in some epithelial malignancies. However the expression profile and the role of clinicopathological significance and therapeutic target potential in medulloblastoma still remain elusive. Currently we detected the expression of Folr1 in medulloblastoma and identified the diagnostic application by evaluating the clinical, pathological and neuroimaging values. Then we developed a target therapeutic compound with Folr1, which exhibited promising efficiency in treatment of medulloblastoma. Folr1 expression was up-regulated in medulloblastoma and positively correlated with percentage of Ki-67 and MMP9 labeling, pathological subtypes, serum Folr1 levels and CSF spreading on MRI. The level of serum Folr1 showed rational sensitivity and specificity in predicting histological subgroups. Strong Folr1 expression was recommended as the independent value regarding the prognosis of patients with medulloblastoma. Folr1 targeted therapy attenuated the tumor growth and metastasis with down-regulation of MMPs proteins and activation of apoptosis. Immunostaining analysis in the xenograft samples showed the decreased Ki-67 and MMP9 index providing the strong evidences that Folr1 targeted application can suppress the proliferation and invasion. Our findings uncovered in Folr1 a predictive candidate and therapeutic target for medulloblastoma.
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Affiliation(s)
- Hailong Liu
- Department of Neurosurgery, Sanbo Brain Hospital Capital Medical University, Beijing, P.R. China.,State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Qianwen Sun
- Department of Neurology, Qilu Hospital Shandong University, Jinan, P.R. China
| | - Mingshan Zhang
- Department of Neurosurgery, Sanbo Brain Hospital Capital Medical University, Beijing, P.R. China
| | - Zhihua Zhang
- Department of Neurosurgery, Sanbo Brain Hospital Capital Medical University, Beijing, P.R. China.,State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Xinyi Fan
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Hongyu Yuan
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Cheng Li
- Department of Neurosurgery, Sanbo Brain Hospital Capital Medical University, Beijing, P.R. China
| | - Yuduo Guo
- Department of Neurosurgery, Sanbo Brain Hospital Capital Medical University, Beijing, P.R. China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital Capital Medical University, Beijing, P.R. China
| | - Youliang Sun
- School of Basic Medical Science, Capital Medical University, Beijing, P.R. China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Chunjiang Yu
- Department of Neurosurgery, Sanbo Brain Hospital Capital Medical University, Beijing, P.R. China
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Iermak IL, Kruglova OB, Palchykovska LH, Alexeeva IV. Spectrophotometrical study of mechanisms of cytidine analogues and ethidium bromide binding with DNA. ACTA ACUST UNITED AC 2007. [DOI: 10.7124/bc.000788] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ie. L. Iermak
- Kharkiv National University
- A. Usikov Institute of Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - O. B. Kruglova
- A. Usikov Institute of Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - L. H. Palchykovska
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - I. V. Alexeeva
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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Hartman WR, Walters DE, Hentosh P. Presence of the anti-leukemic nucleotide analog, 2-chloro-2'-deoxyadenosine-5'-monophosphate, in a promoter sequence alters DNA binding of TATA-binding protein (TBP). Arch Biochem Biophys 2007; 459:223-32. [PMID: 17320040 DOI: 10.1016/j.abb.2006.12.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 12/12/2006] [Accepted: 12/29/2006] [Indexed: 11/19/2022]
Abstract
2-Chlorodeoxyadenosine (CldAdo, Cladribine), a nucleoside analog used in the treatment of hairy cell leukemia, is phosphorylated and incorporated into DNA, but is not an absolute chain terminator. We hypothesized that the presence of a chlorine molecule projecting into the DNA minor groove would affect DNA:protein-binding interactions. Here, we investigated recognition of and binding to double-stranded CldAMP-substituted TATA promoter sequences by human TATA-binding protein (TBP) using mobility shift assays. Depending on the site, CldAMP in place of dAMP within a TATA sequence decreased in vitro TBP binding by approximately 30% to 55% compared to control sites. When bound to a CldAMP-substituted TATA box, however, the TBP complex was more resistant to polyanions, suggesting enhanced stability. Limited exposure of the TBP:DNA complex to proteases indicated that TBP conformation was altered on CldAMP-substituted DNA compared to control. Further, binding of transcription factor IIB to TBP was diminished on analog-containing TATA sequences. These results suggest normal TBP-binding interactions--specifically recognition, stability, and conformation-are disrupted by CldAMP insertion into eukaryotic promoter sequences.
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Affiliation(s)
- William R Hartman
- Department of Pharmacology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
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Colón-Cesario M, Wang J, Ramos X, García HG, Dávila JJ, Laguna J, Rosado C, Peña de Ortiz S. An inhibitor of DNA recombination blocks memory consolidation, but not reconsolidation, in context fear conditioning. J Neurosci 2006; 26:5524-33. [PMID: 16707804 PMCID: PMC6675301 DOI: 10.1523/jneurosci.3050-05.2006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Genomic recombination requires cutting, processing, and rejoining of DNA by endonucleases, polymerases, and ligases, among other factors. We have proposed that DNA recombination mechanisms may contribute to long-term memory (LTM) formation in the brain. Our previous studies with the nucleoside analog 1-beta-D-arabinofuranosylcytosine triphosphate (ara-CTP), a known inhibitor of DNA ligases and polymerases, showed that this agent blocked consolidation of conditioned taste aversion without interfering with short-term memory (STM). However, because polymerases and ligases are also essential for DNA replication, it remained unclear whether the effects of this drug on consolidation were attributable to interference with DNA recombination or neurogenesis. Here we show, using C57BL/6 mice, that ara-CTP specifically blocks consolidation but not STM of context fear conditioning, a task previously shown not to require neurogenesis. The effects of a single systemic dose of cytosine arabinoside (ara-C) on LTM were evident as early as 6 h after training. In addition, although ara-C impaired LTM, it did not impair general locomotor activity nor induce brain neurotoxicity. Importantly, hippocampal, but not insular cortex, infusions of ara-C also blocked consolidation of context fear conditioning. Separate studies revealed that context fear conditioning training significantly induced nonhomologous DNA end joining activity indicative of DNA ligase-dependent recombination in hippocampal, but not cortex, protein extracts. Finally, unlike inhibition of protein synthesis, systemic ara-C did not block reconsolidation of context fear conditioning. Our results support the idea that DNA recombination is a process specific to consolidation that is not involved in the postreactivation editing of memories.
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