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Wang T, Zhao X, Liu T, Zhang J, Qiu J, Li M, Weng R. Transcriptional investigation of the toxic mechanisms of perfluorooctane sulfonate in rats based on an RNA-Seq approach. CHEMOSPHERE 2023; 329:138629. [PMID: 37030344 DOI: 10.1016/j.chemosphere.2023.138629] [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: 10/09/2021] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Perfluorooctane sulfonate (PFOS) was widely used in industrial applications before it was listed as a persistent organic pollutant by the Conference of the Parties in the Stockholm Convention in 2009. Although the potential toxicity of PFOS has been studied, its toxic mechanisms remain largely undefined. Here, we investigated novel hub genes and pathways affected by PFOS to gain new conceptions of the toxic mechanisms of PFOS. Reduced body weight gain and abnormal ultra-structures in the liver and kidney tissues were spotted in PFOS-exposed rats, indicating successful establishment of the PFOS-exposed rat model. The transcriptomic alterations of blood samples upon PFOS exposure were analysed using RNA-Seq. GO analysis indicates that the differentially expressed gene-enriched GO terms are related to metabolism, cellular processes, and biological regulation. Kyoto encyclopaedia of gene and genomes (KEGG) and gene set enrichment analysis (GSEA) were conducted to identify six key pathways: spliceosome, B cell receptor signalling pathway, acute myeloid leukaemia, protein processing in the endoplasmic reticulum, NF-kappa B signalling pathway, and Fc gamma R-mediated phagocytosis. The top 10 hub genes were screened from a protein-protein interaction network and verified via quantitative real-time polymerase chain reaction. The overall pathway network and hub genes may provide new insights into the toxic mechanisms of PFOS exposure states.
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Affiliation(s)
- Tianrun Wang
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Xuying Zhao
- Key Laboratory of Quality and Risk Assessment for Tobacco and Aromatic Plant Products (Qingdao) of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, China
| | - Tianze Liu
- Key Laboratory of Quality and Risk Assessment for Tobacco and Aromatic Plant Products (Qingdao) of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, China
| | - Jiguang Zhang
- Key Laboratory of Quality and Risk Assessment for Tobacco and Aromatic Plant Products (Qingdao) of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, China
| | - Jing Qiu
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mei Li
- College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Rui Weng
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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The RPB2 flap loop of human RNA polymerase II is dispensable for transcription initiation and elongation. Mol Cell Biol 2011; 31:3312-25. [PMID: 21670157 DOI: 10.1128/mcb.05318-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The flap domain of multisubunit RNA polymerases (RNAPs), also called the wall, forms one side of the RNA exit channel. In bacterial RNAP, the mobile part of the flap is called the flap tip and makes essential contacts with initiation and elongation factors. Cocrystal structures suggest that the orthologous part of eukaryotic RNAPII, called the flap loop, contacts transcription factor IIB (TFIIB), but the function of the flap loop has not been assessed. We constructed and tested a deletion of the flap loop in human RNAPII (subunit RPB2 Δ873-884) that removes the flap loop interaction interface with TFIIB. Genome-wide analysis of the distribution of the RNAPII with the flap loop deletion expressed in a human embryonic kidney cell line (HEK 293) revealed no effect of the flap loop on global transcription initiation, RNAPII occupancy within genes, or the efficiency of promoter escape and productive elongation. In vitro, the flap loop deletion had no effect on promoter binding, abortive initiation or promoter escape, TFIIS-stimulated transcript cleavage, or inhibition of transcript elongation by the complex of negative elongation factor (NELF) and 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB) sensitivity-inducing factor (DSIF). A modest effect on transcript elongation and pausing was suppressed by TFIIF. Although similar to the flap tip of bacterial RNAP, the RNAPII flap loop is not equivalently essential.
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Asgari S, Davis J, Wood D, Wilson P, McGrath A. Sequence and organization of the Heliothis virescens ascovirus genome. J Gen Virol 2007; 88:1120-1132. [PMID: 17374755 DOI: 10.1099/vir.0.82651-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleotide sequence of the Heliothis virescens ascovirus (HvAV-3e) DNA genome was determined and characterized in this study. The circular genome consists of 186,262 bp, has a G+C content of 45.8 mol% and encodes 180 potential open reading frames (ORFs). Five unique homologous regions (hrs), 23 'baculovirus repeat ORFs' (bro) and genes encoding a caspase homologue and several enzymes involved in nucleotide replication and metabolism were found in the genome. Several ascovirus (AV)-, iridovirus- and baculovirus-homologous genes were identified. The genome is significantly larger than the recently sequenced genomes of Trichoplusia ni AV (TnAV-2c) and Spodoptera frugiperda AV (SfAV-1a). Gene-parity plots and overall similarity of ORFs indicate that HvAV-3e is related more closely to SfAV-1a than to TnAV-2c.
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Affiliation(s)
- Sassan Asgari
- School of Integrative Biology, University of Queensland, St Lucia, QLD 4072, Australia
| | - John Davis
- Australian Genome Research Facility, University of Queensland, St Lucia, QLD 4072, Australia
| | - David Wood
- Australian Genome Research Facility, University of Queensland, St Lucia, QLD 4072, Australia
| | - Peter Wilson
- Australian Genome Research Facility, University of Queensland, St Lucia, QLD 4072, Australia
| | - Annette McGrath
- Australian Genome Research Facility, University of Queensland, St Lucia, QLD 4072, Australia
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Wang L, Xue J, Seaborn CP, Arif BM, Cheng XW. Sequence and organization of the Trichoplusia ni ascovirus 2c (Ascoviridae) genome. Virology 2006; 354:167-77. [PMID: 16876847 DOI: 10.1016/j.virol.2006.06.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 06/19/2006] [Accepted: 06/22/2006] [Indexed: 10/24/2022]
Abstract
The complete Trichoplusia ni ascovirus 2c (TnAV-2c) genome sequence was determined. The circular genome contains 174,059 bp with 165 open reading frames (ORFs) of greater than 180 bp and two major homologous regions (hrs). The genome is quite A+T rich at 64.6%. Fifty-four ORFs had homologues in other insect viruses, such as ascoviruses, iridoviruses, baculoviruses and entomopoxviruses; 30 ORFs showed low identities with those from different parasitic protozoa and 12 ORFs were unique to TnAV-2c. TnAV-2c has 15 ORFs that could be grouped into six gene families. Three major conserved repeating sequences were identified and were interspersed in two regions. BLAST analyses revealed that there were 16 enzymes involved in gene transcription, DNA replication, and nucleotide metabolism. TnAV-2c has 12 and 25 ORFs sharing high identities with ascovirus and iridovirus homologues, respectively. The codon usage bias appears to be more similar to Spodoptera frugiperda ascovirus 1a than to iridoviruses.
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Affiliation(s)
- Lihua Wang
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, OH 45056, USA
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