ZBED6基因敲除猪肾脏转录组分析

doi:10.16431/j.cnki.1671-7236.2022.05.007

Abstract

Abstract: 【Objective】 This study was aimed to investigate the effect of zinc finger BED domain-containing protein 6 (ZBED6) gene knockout on gene transcription and expression in porcine kidney,and analyze the target genes and pathways of ZBED6 gene regulating porcine kidney metabolism.【Method】 Kidney tissues were collected from 8-month-old ZBED6 gene knockout Bama Xiang pigs (ZBED6 KO) and age-matched wildtype Bama Xiang pigs (WT) (n=3).The total RNA was extracted and Real-time quantitative PCR was used to analyze the expression of insulin-like growth factor 2 (IGF2) and other differentially expressed genes.Illumina Hiseq high-throughput sequencing technology was performed to evaluate the mRNA of kidney in ZBED6 Ko and WT pigs.Sus scrofa 11.1 was used as the reference genome sequence,the differentially expressed genes were analyzed and filtered by the softwares TopHat,Cufflink,Cuffmerge and Cuffdiff.Hierarchical clustering analysis and KEGG pathway enrichment of the differentially expressed genes were also performed.The reliability of differentially expressed genes in RNA-Seq results was verified by Real-time quantitative PCR.【Result】 Real-time quantitative PCR results showed that the expression of IGF2 gene mRNA in kidney of ZBED6 KO pigs was significantly higher than that of WT pigs (P<0.05).The sequencing results showed that 78 G data was obtained,and at least 87.3% of the reads were mapped to porcine genome,suggesting the quality of sequencing was high.RNA-Seq analysis showed that a total of 25 213 genes were detected in kidney of WT and ZBED6 KO pigs.Under the criteria of adjust-P<0.05 and log₂|FoldChange|>2,299 differentially expressed genes were obtained,including 103 up-regulated genes and 199 down-regulated genes.Heatmap and PCA results showed that the gene expression pattern was similar within groups,and was different between groups.KEGG pathway enrichment analysis displayed that the differentially expressed genes were mainly involved in retinol and other metabolic pathways,especially,9 differentially expressed genes were enriched to the retinol metabolism pathway,including CYP2C42,AOX1,ENSSSCG00000036274,RDH16,CYP2A19,ENSSSCG00000022724,CYP26B1,CYP1A1 and RDH5,7 genes (CYP2C42,AOX1,RDH16,CYP2A19,CYP26B1,CYP1A1 and RDH5) of which were further validated by Real-time quantitative RCR,confirmed the reliability of RNA-Seq results.【Conclusion】 The effect of ZBED6 gene knockout on kidney metabolism of Bama Xiang pigs was analyzed by RNA-Seq technology in this study,it affected its metabolic related signal pathway by regulating the expression of multiple downstream genes in kidney,which provided materials for clarifying the function of ZBED6 gene.

Key words: pigs; ZBED6 gene; kidney; metabolism; RNA-Seq; differentially expressed genes

CLC Number:

TIAN Wenjie, WANG Dandan, WANG Shengnan, MA Yuehui, JIANG Lin, SONG Ziyi. Transcriptome Analysis of Porcine Kidney with ZBED6 Gene Deletion[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(5): 1662-1670.

References

[1] MARKLJUNG E,JIANG L,JAFFE J D,et al.ZBED6,a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth[J].PLoS Biology,2009,7(12):e1000256.
[2] JEON J T,CARLBORG O,TORNSTEN A,et al.A paternally expressed QTL affecting skeletal and cardiac muscle mass in pigs maps to the IGF2 locus[J].Nature Genetics,1999,21(2):157-158.
[3] WANG D,PAN D,XIE B,et al.Porcine ZBED6 regulates growth of skeletal muscle and internal organs via multiple targets[J].PLoS Genetics,2021,17(10):e1009862.
[4] HUANG Y Z,ZHAN Z Y,SUN Y J,et al.Comparative analysis of the IGF2 and ZBED6 gene variants and haplotypes reveals significant effect of growth traits in cattle[J].Genome,2013,56(6):327-334.
[5] HUANG Y Z,HE H,ZHAN Z Y,et al.Relationship of polymorphisms within ZBED6 gene and growth traits in beef cattle[J].Gene,2013,526(2):107-111.
[6] 马燕,贺三刚,李文蓉.绵羊ZBED6基因多态性检测及群体遗传结构分析[J].石河子大学学报(自然科学版),2016,34(4):431-435. MA Y,HE S G,LI W R.Study on the polymorphisms and population genetic structure analysis of ZBED6 gene in two different sheep breeds[J].Journal of Shihezi University(Natural Science),2016,34(4):431-435.(in Chinese)
[7] YOUNIS S,SCHONKE M,MASSART J,et al.The ZBED6-IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals[J].Proceedings of the National Academy of Sciences of the United States of America,2018,115(9):E2048-E2057.
[8] HUANG Y Z,ZHANG L Z,LAI X S,et al.Transcription factor ZBED6 mediates IGF2 gene expression by regulating promoter activity and DNA methylation in myoblasts[J].Scientific Reports,2014,4:4570.
[9] JIANG L,WALLERMAN O,YOUNIS S,et al.ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells[J].PLoS One,2014,9(4):e94187.
[10] LIU X,QIU S,MEI L,et al.A high-resolution melting analysis with an unlabeled probe for CRISPR/Cas9-induced ZBED6 knockout pigs detection[J].Journal of Aoac International,2021,104(3):541-545.
[11] WANG X,JIANG L,WALLERMAN O,et al.Transcription factor ZBED6 affects gene expression,proliferation,and cell death in pancreatic beta cells[J].Proceedings of the National Academy of Sciences of the United States of America,2013,110(40):15997-16002.
[12] WANG X,YOUNIS S,CEN J,et al.ZBED6 counteracts high-fat diet-induced glucose intolerance by maintaining beta cell area and reducing excess mitochondrial activation[J].Diabetologia,2021,64(10):2292-2305.
[13] WANG X,JIANG L,WALLERMAN O,et al.ZBED6 negatively regulates insulin production,neuronal differentiation,and cell aggregation in MIN6 cells[J].FASEB Journal,2019,33(1):88-100.
[14] AKHTAR A M,YOUNIS S,WALLERMAN O,et al.Transcriptional modulator ZBED6 affects cell cycle and growth of human colorectal cancer cells[J].Proceedings of the National Academy of Sciences of the United States of America,2015,112(25):7743-7748.
[15] OLSEN T,BLOMHOFF R.Retinol,retinoic acid,and retinol-binding protein 4 are differentially associated with cardiovascular disease,type 2 diabetes,and obesity:An overview of human studies[J].Advances in Nutrition,2020,11(3):644-666.
[16] MODY N.Alterations in vitamin A/retinoic acid homeostasis in diet-induced obesity and insulin resistance[J].Proceedings of the Nutrition Society,2017,76(4):597-602.
[17] RAILA J,BUCHHOLZ I,AUPPERLE H,et al.The distribution of vitamin A and retinol-binding protein in the blood plasma,urine,liver and kidneys of carnivores[J].Veterinary Research,2000,31(6):541-551.
[18] GERLACH T H,ZILE M H.Metabolism and secretion of retinol transport complex in acute renal failure[J].Journal of Lipid Research,1991,32(3):515-520.
[19] GAVRILOV V,HARMAN-BOEHM I,AMICHAY D,et al.Kidney function and retinol status in type 2 diabetes mellitus patients[J].Acta Diabetologica,2012,49(2):137-143.
[20] DUESTER G,FARRES J,FELDER M R,et al.Recommended nomenclature for the vertebrate alcohol dehydrogenase gene family[J].Biochemical Pharmacology,1999,58(3):389-395.
[21] PERSSON B,KALLBERG Y,BRAY J E,et al.The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative[J].Chemico-Biological Interactions,2009,178(1-3):94-98.
[22] JEZ J M,FLYNN T G,PENNING T M.A new nomenclature for the aldo-keto reductase superfamily[J].Biochemical Pharmacology,1997,54(6):639-647.
[23] PEROZICH J,NICHOLAS H,WANG B C,et al.Relationships within the aldehyde dehydrogenase extended family[J].Protein Science,1999,8(1):137-146.
[24] XIAO S,DENG Y,SHEN N,et al.Curc-mPEG454,a PEGylated curcumin derivative,as a multi-target anti-fibrotic prodrug[J].International Immunopharmacology,2021,101(Pt A):108166.
[25] SNYDER J M,ZHONG G,HOGARTH C,et al.Knockout of Cyp26a1 and Cyp26b1 during postnatal life causes reduced lifespan,dermatitis,splenomegaly,and systemic inflammation in mice[J].FASEB Journal,2020,34(12):15788-15804.
[26] KRIVOSPITSKAYA O,ELMABSOUT A A,SUNDMAN E,et al.A CYP26B1 polymorphism enhances retinoic acid catabolism and may aggravate atherosclerosis[J].Molecular Medicine,2012,18:712-718.
[27] BELYAEVA O V,JOHNSON M P,KEDISHVILI N Y.Kinetic analysis of human enzyme RDH10 defines the characteristics of a physiologically relevant retinol dehydrogenase[J].Journal of Biological Chemistry,2008,283(29):20299-20308.
[28] KAO Y H,LEE P H,CHIU T C,et al.Transcriptome analysis reveals a positive role for nerve growth factor in retinol metabolism in primary rat hepatocytes[J].Cytokine,2018,107:74-78.
[29] NAPOLI J L.Interactions of retinoid binding proteins and enzymes in retinoid metabolism[J].Biochim Biophys Acta,1999,1440(2-3):139-162.
[30] DRIESSEN C,WINKENS H J,HOFFMANN K,et al.Disruption of the 11-cis-retinol dehydrogenase gene leads to accumulation of cis-retinols and cis-retinyl esters[J].Molecular and Cellular Biology,2000,20(12):4275-4287.
[31] SHANG E,LAI K,PACKER A I,et al.Targeted disruption of the mouse cis-retinol dehydrogenase gene:Visual and nonvisual functions[J].Journal of Lipid Research,2002,43(4):590-597.
[32] YAMAMOTO H,SIMON A,ERIKSSON U,et al.Mutations in the gene encoding 11-cis retinol dehydrogenase cause delayed dark adaptation and fundus albipunctatus[J].Nature Genetics,1999,22(2):188-191.
[33] ZHANG Q Y,DUNBAR D,KAMINSKY L.Human cytochrome P-450 metabolism of retinals to retinoic acids[J].Drug Metabolism and Disposition,2000,28(3):292-297.
[34] CHOUDHARY D,JANSSON I,STOILOV I,et al.Metabolism of retinoids and arachidonic acid by human and mouse cytochrome P450 1b1[J].Drug Metabolism and Disposition,2004,32(8):840-847.
[35] LAMPEN A,MEYER S,ARNHOLD T,et al.Metabolism of vitamin A and its active metabolite all-trans-retinoic acid in small intestinal enterocytes[J].Journal of Pharmacology and Experimental Therapeutics,2000,295(3):979-985.
[36] ELOVAARA E,VAINIO H,PFAFFLI P,et al.Effects of intermittent styrene inhalation,ethanol intake and their combination on drug biotransformation in rat liver and kidneys[J].Medical Biology,1979,57(5):321-327.

Transcriptome Analysis of Porcine Kidney with ZBED6 Gene Deletion

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	WEI Mingbang, BIANBA Qiongda, XIAO Qingqing, DUAN Mengqi, CHAMBA Yangzom, SHANG Peng. Cloning,Bioinformatics and Expression Analysis of CDKN1B Gene in Tibetan Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2196-2206.
[2]	ZHANG Fangwei, ZHANG Qi, LEI Liangliang, SUN Wusheng, ZHANG Di, ZHANG Yunpeng, ZHANG Jingbo, WANG Xiuquan, ZHANG Jing, ZHANG Shumin. Polymorphism of HBEGF Gene and Its Association with Reproductive Traits in Songliao Black Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2370-2379.
[3]	PAN Pengcheng, LEI Zongquan, LI Xian, HU Xiangyun, QIN Qiantao, QIN Zhaoxian, GUAN Zhihui, CHEN Baojian, XIE Bingkun. Bioinformatics Analysis,Eukaryotic Expression Vector Construction and Tissue Expression of MYL2 Gene in Luchuan Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1796-1806.
[4]	LIU Hongrun, ZHU Siran, FENG Lingli, ZHANG Kun, YAN Gang, WANG Yubin, ZHANG Shuai, JIANG Shan, XU Di, LAN Ganqiu, LIANG Jing. Cloning,Bioinformatics Analysis and Tissue Expression Localization of CDO1 Gene in Large White Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1352-1363.
[5]	CHANG Yitong, ZHANG Wei, PENG Yinglin, CHEN Chen. Evolutionary Analysis,Target Gene Prediction and Tissue Expression Analysis of miR-192 [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 882-892.
[6]	FANG Qinyuan, FU Shaoyin, WANG Biao, HE Xiaolong, HE Jiangfeng, WANG Liwei, CHEN Xin, ZHANG Lin, WANG Daqing, MA Yuejun, ZHANG Liling, LIU Yongbin. Research Progress on Influencing Factors of Brown Fat Activity in Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 1059-1067.
[7]	SUN Yanyong, MA Fengying, GUO Lili, LIU Zaixia, LIU Bin, ZHANG Wenguang, LIU Yongbin. Advances on the Application of Animal Blood Transcriptome [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 460-468.
[8]	YIN Yi, LYU Yanqiu, CHEN Xuan, CAO Lipeng, ZHANG Junzheng, JIN Yi. Effects of Capacitation on Sperm Quality and Regulation of Acrosin Inhibitor Levels by Ubiquitin in Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(1): 174-185.
[9]	CHEN Chuanhe, LIU Jiali, ZHANG Lilan, ZHAO Ying, TAO Cong. Bioinformatics Analysis of Porcine SGK Family Genes and Their Expression in Porcine Adipose Tissues and Adipocytes [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3310-3320.
[10]	WO Yeqianli, GAO Duo, MA Fengtao, JIN Yuhang, LIU Zhuo, SUN Peng. Effects of Two Different Organic Zinc Sources Supplementation on Growth Performance and Zinc Metabolism of Newborn Heifers [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3382-3390.
[11]	WANG Shuaijie, TAN Zihan, LI Hanbo, SUN Xiangxue, AI Sihan, WANG Lei, ZHAO Di, HOU Yongqing. Effects of Quercetin on Intestinal Morphology, Antioxidant Function and Jejunal Lipid Metabolism Gene Expression in Piglets with Porcine Epidemic Diarrhea Virus [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3391-3399.
[12]	YANG Man, LIU Hai, ZHANG Run, HU Ziping, NIU Naiqi, WANG Lixian, ZHANG Longchao. Association Analysis of Polymorphism of MYH3 and MYH13 Genes with Meat Quality Traits in Beijing Black Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3428-3437.
[13]	YU Peng, NIU Xiaoyu, DONG Ling, LU Mengqi, CHEN Yanhong, LI Fan, SONG Hui. Research Progress on the Role of lncRNA in Porcine Abortion-related Virus Infection [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3559-3568.
[14]	HE Yanjun, JIN Shengzi, WANG Shuang, LIU Kexin, LIU Yun. Relaxation Effect of Diosgenin on Kidney Injury Induced by Cisplatin in Rats [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3633-3642.
[15]	NIE Jingru, MA Li, YAN Dawei, DENG Jun, ZHANG Hao, ZHANG Bo, LIU Jinqiao, DONG Xinxing. Analysis of Differentially Expressed Genes and Regulation Pathways of Intramuscular Fat Deposition in Large Diqing Tibetan Pigs at Different Growth Stages [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2855-2868.