Identification and functional prediction of long non-coding RNAs related to oxidative stress in the jejunum of piglets
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Objective: Oxidative stress (OS) is a pathological process arising from the excessive production of free radicals in the body. It has the potential to alter animal gene expression and cause damage to the jejunum. However, there have been few reports of changes in the expression of long noncoding RNAs (lncRNAs) in the jejunum in piglets under OS. The purpose of this research was to examine how lncRNAs in piglet jejunum change under OS.Methods: The abdominal cavities of piglets were injected with diquat (DQ) to produce OS. Raw reads were downloaded from the SRA database. RNA-seq was utilized to study the expression of lncRNAs in piglets under OS. Additionally, six randomly selected lncRNAs were verified using quantitative real-time polymerase chain reaction (qRT‒PCR) to examine the mechanism of oxidative damage.Results: A total of 79 lncRNAs were differentially expressed (DE) in the treatment group compared to the negative control group. The target genes of DE lncRNAs were enriched in gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) signaling pathways. Chemical carcinogenesis-reactive oxygen species, the Foxo signaling pathway, colorectal cancer, and the AMPK signaling pathway were all linked to OS.Conclusion: Our results demonstrated that DQ-induced OS causes differential expression of lncRNAs, laying the groundwork for future research into the processes involved in the jejunum’s response to OS.
Abstract
Objective: Oxidative stress (OS) is a pathological process arising from the excessive production of free radicals in the body. It has the potential to alter animal gene expression and cause damage to the jejunum. However, there have been few reports of changes in the expression of long noncoding RNAs (lncRNAs) in the jejunum in piglets under OS. The purpose of this research was to examine how lncRNAs in piglet jejunum change under OS. Methods: The abdominal cavities of piglets were injected with diquat (DQ) to produce OS. Raw reads were downloaded from the SRA database. RNA-seq was utilized to study the expression of lncRNAs in piglets under OS. Additionally, six randomly selected lncRNAs were verified using quantitative real-time polymerase chain reaction (qRT‒PCR) to examine the mechanism of oxidative damage. Results: A total of 79 lncRNAs were differentially expressed (DE) in the treatment group compared to the negative control group. The target genes of DE lncRNAs were enriched in gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) signaling pathways. Chemical carcinogenesis-reactive oxygen species, the Foxo signaling pathway, colorectal cancer, and the AMPK signaling pathway were all linked to OS. Conclusion: Our results demonstrated that DQ-induced OS causes differential expression of lncRNAs, laying the groundwork for future research into the processes involved in the jejunum’s response to OS.
참고문헌 (49)
- Sies H, "Oxidative stress : a concept in redox biology and medicine", Redox Biol, 4, pp.180~183 (2015)[DOI]
- Li Z, "The role of oxidative stress in acute ischemic stroke-related thrombosis", Oxid Med Cell Longev, 2022, pp.8418820~ (2022)[DOI]
- Srinivas US, "Ros and the dna damage response in cancer", Redox Biol, 25, pp.101084~ (2019)[DOI]
- Burton GJ, "Oxidative stress", Best Pract Res Clin Obstet Gynaecol, 25, pp.287~299 (2011)[DOI]
- Aw TY, "Intestinal glutathione : determinant of mucosal peroxide transport, metabolism, and oxidative susceptibility", Toxicol Appl Pharmacol, 204, pp.320~328 (2005)[DOI]
- Luissint A, "Inflammation and the intestinal barrier : leukocyte–epithelial cell interactions, cell junction remodeling, and mucosal repair", Gastroenterology, 151, pp.616~632 (2016)[DOI]
- Zheng P, "Protective effects of dietary arginine supplementation against oxidative stress in weaned piglets", Br J Nutr, 109, pp.2253~2260 (2013)[DOI]
- Cao S, "Diquat-induced oxidative stress increases intestinal permeability, impairs mitochondrial function, and triggers mitophagy in piglets", J Anim Sci, 96, pp.1795~1805 (2018)[DOI]
- Amaral PP, "Non-coding rnas in homeostasis, disease and stress responses : an evolutionary perspective", Brief Funct Genomics, 12, pp.254~278 (2013)[DOI]
- Ma Q, "Transcriptional responses to oxidative stress : pathological and toxicological implications", Pharmacol Ther, 125, pp.376~393 (2010)[DOI]
- Bonasio R, "Regulation of transcription by long noncoding rnas", Annu Rev Genet, 48, pp.433~455 (2014)[DOI]
- Quinodoz S, "Long noncoding rnas : an emerging link between gene regulation and nuclear organization", Trends Cell Biol, 24, pp.651~663 (2014)[DOI]
- Fatica A, "Long non-coding rnas : new players in cell differentiation and development", Nat Rev Genet, 15, pp.7~21 (2014)[DOI]
- Tehrani SS, "Multiple functions of long non-coding rnas in oxidative stress, dna damage response and cancer progression", J Cell Biochem, 119, pp.223~236 (2018)[DOI]
- Gao Q, "Melatonin attenuates h2o2-induced oxidative injury by upregulating lncrna neat1 in ht22 hippocampal cells", Int J Mol Sci, 23, pp.12891~ (2022)[DOI]
- Xie W, "Lncrna h19 inhibits oxidative stress injury of cochlear hair cells by regulating mir-653-5p", sirt1 axis, 2022, pp.54, 332~339
- Magalhaes N, "Human and experimental toxicology of diquat poisoning : toxicokinetics, mechanisms of toxicity, clinical features, and treatment", Hum Exp Toxicol, 37, pp.1131~1160 (2018)[DOI]
- Li Z, "Characteristics of circrnas expression profiles in the piglets intestine induced by oxidative stress", Genes Genomics, 44, pp.425~433 (2022)[DOI]
- Chen S, "Fastp : an ultra-fast all-in-one fastq preprocessor", Bioinformatics, 34, pp.i884~i890 (2018)[DOI]
- Kim D, "Hisat : a fast spliced aligner with low memory requirements", Nat Methods, 12, pp.357~360 (2015)[DOI]
- Pertea M, "Stringtie enables improved reconstruction of a transcriptome from rna-seq reads", Nat Biotechnol, 33, pp.290~295 (2015)[DOI]
- Liao Y, "Featurecounts : an efficient general purpose program for assigning sequence reads to genomic features", Bioinformatics, 30, pp.923~930 (2014)[DOI]
- "F1000Res", 2020, 304~, 10.12688[DOI]
- Kang Y, "Cpc2 : a fast and accurate coding potential calculator based on sequence intrinsic features", Nucleic Acids Res, 45, pp.W12~W16 (2017)[DOI]
- Sun L, "Utilizing sequence intrinsic composition to classify protein-coding and long non-codin transcripts", Nucleic Acids Res, 41, pp.e166~ (2013)[DOI]
- Mistry J, "Pfam : the protein families database in 2021", Nucleic Acids Res, 49, pp.D412~D419 (2021)[DOI]
- Love MI, "Moderated estimation of fold change and dispersion for rna-seq data with deseq2", Genome Biol, 15, pp.550~ (2014)[DOI]
- Quinlan AR, "Bedtools : a flexible suite of utilities for comparing genomic features", Bioinformatics, 26, pp.841~842 (2010)[DOI]
- Venkatesan A, "Identification of novel lncrna by reanalysis of rna-seq data in zika virus infected hinpcs", Virusdisease, 33, pp.185~193 (2022)[DOI]
- Mukaka MM, "Statistics corner : a guide to appropriate use of correlation coefficient in medical research", Malawi Med J, 24, pp.69~71 (2012)
- Sherman BT, "David : a web server for functional enrichment analysis and functional annotation of gene lists(2021 update)", Nucleic Acids Res, 50, pp.W216~W221 (2022)[DOI]
- Florea L, "Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues", F1000Res, 2, pp.188~ (2013)[DOI]
- Schmittgen TD, "Analyzing real-time pcr data by the comparative ct method", Nat Protoc, 3, pp.1101~1108 (2008)[DOI]
- Gou HZ, "How do intestinal probiotics restore the intestinal barrier?", Front Microbiol, 13, pp.929346~ (2022)[DOI]
- Li Z, "Characteristics of circrnas expression profiles in the piglets intestine induced by oxidative stress", Genes Genomics, 44, pp.425~433 (2022)[DOI]
- Wang J, "Diquat determines a deregulation of lncrna and mrna expression in the liver of postweaned piglets", Oxid Med Cell Longev, 2019, pp.9148535~ (2019)[DOI]
- Yuan S, "Effects of oxidative stress on growth performance, nutrient digestibilities and activities of antioxidative enzymes of weanling pigs", Asian-Australas J Anim Sci, 20, pp.1600~1605 (2007)[DOI]
- Zheng P, "Effects of oxidative stress induced by diquat on arginine metabolism of postweaning pigs", Asian-Australas J Anim Sci, 23, pp.98~105 (2010)[DOI]
- Zhang TN, "Regulation of glucose and lipid metabolism by long non-coding rnas : facts and research progress", Front Endocrinol(Lausanne), 11, pp.457~ (2020)[DOI]
- Wang S, "The role of lncrna pcat6 in cancers", Front Oncol, 11, pp.701495~ (2021)[DOI]
- Ma L, "Identification and functional prediction of long non-coding rnas related to skeletal muscle development in duroc pigs", Anim Biosci, 35, pp.1512~1523 (2022)[DOI]
- Moon KM, "Foxo6 inhibits melanogenesis partly by elevating intracellular antioxidant capacity", Redox Biol, 36, pp.101624~ (2020)[DOI]
- Bang E, "Protease-activated receptor 2induces ros-mediated inflammation through akt-mediated nf-κb and foxo6 modulation during skin photoaging", Redox Biol, 44, pp.102022~ (2021)[DOI]
- Xu J, "Activation of ampk by osu53 protects spinal cord neurons from oxidative stress", Oncotarget, 8, pp.112477~112486 (2017)[DOI]
- Maharajan N, "Licochalcone d ameliorates oxidative stress-induced senescence via ampk activation", Int J Mol Sci, 22, pp.7324~ (2021)[DOI]
- Singh V, "Role of silent information regulator 1(sirt1)in regulating oxidative stress and inflammation", Inflammation, 43, pp.1589~1598 (2020)[DOI]
- Basak D, "The role of oxidative stress and its counteractive utility in colorectal cancer(crc)", Cancers(Basel), 12, pp.3336~ (2020)[DOI]
- Carini F, "Colorectal carcinogenesis : role of oxidative stress and antioxidants", Anticancer Res, 37, pp.4759~4766 (2017)[DOI]
- Bian Y, "Development of sos1 inhibitor based degraders to targetkras-mutant colorectal cancer", J Med Chem, 65, pp.16432~16450 (2022)[DOI]