DOI QR코드

DOI QR Code

Circular RNA expression profiles in the porcine liver of two distinct phenotype pig breeds

  • Huang, Minjie ;
  • Shen, Yifei ;
  • Mao, Haiguang ;
  • Chen, Lixing ;
  • Chen, Jiucheng ;
  • Guo, Xiaoling ;
  • Xu, Ningying
  • Received : 2017.09.07
  • Accepted : 2017.11.30
  • Published : 2018.06.01

Abstract

Objective: An experiment was conducted to identify and characterize the circular RNA expression and metabolic characteristics in the liver of Jinhua pigs and Landrace pigs. Methods: Three Jinhua pigs and three Landrace pigs respectively at 70-day were slaughtered to collect the liver tissue samples. Immediately after slaughter, blood samples were taken to detect serum biochemical indicators. Total RNA extracted from liver tissue samples were used to prepare the library and then sequence on HiSeq 2500. Bioinformatic methods were employed to analyze sequence data to identify the circRNAs and predict the potential roles of differentially expressed circRNAs between the two breeds. Results: Significant differences in physiological and biochemical traits were observed between growing Jinhua and Landrace pigs. We identified 84,864 circRNA candidates in two breeds and 366 circRNAs were detected as significantly differentially expressed. Their host genes are involved in lipid biosynthetic and metabolic processes according to the gene ontology analysis and associated with metabolic pathways. Conclusion: Our research represents the first description of circRNA profiles in the porcine liver from two divergent phenotype pigs. The predicted miRNA-circRNA interaction provides important basis for miRNA-circRNA relationships in the porcine liver. These data expand the repertories of porcine circRNA and are conducive to understanding the possible molecular mechanisms involved in miRNA and circRNA. Our study provides basic data for further research of the biological functions of circRNAs in the porcine liver.

Keywords

Circular RNA;Liver;Pig;RNA-seq

References

  1. Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci USA 1976;73:3852-6. https://doi.org/10.1073/pnas.73.11.3852
  2. Burd CE, Jeck WR, Liu Y, et al. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. Plos Genet 2010;6:e1001233. https://doi.org/10.1371/journal.pgen.1001233
  3. Veno MT, Hansen TB, Veno ST, et al. Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. Genome Biol 2015;16:245. https://doi.org/10.1186/s13059-015-0801-3
  4. Cocquerelle C, Mascrez B, Hetuin D, Bailleul B. Mis-splicing yields circular RNA molecules. FASEB J 1993;7:155-60. https://doi.org/10.1096/fasebj.7.1.7678559
  5. Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol 2014;32:453-61. https://doi.org/10.1038/nbt.2890
  6. Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013;495:333-8. https://doi.org/10.1038/nature11928
  7. Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature 2013;495:384-8. https://doi.org/10.1038/nature11993
  8. Zhang Y, Zhang XO, Chen T, et al. Circular intronic long noncoding RNAs. Mol Cell 2013;51:792-806. https://doi.org/10.1016/j.molcel.2013.08.017
  9. Pamudurti NR, Bartok O, Jens M, et al. Translation of CircRNAs. Mol Cell 2017;66:9-21.e7. https://doi.org/10.1016/j.molcel.2017.02.021
  10. Legnini I, Di TG, Rossi F, et al. Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis. Mol Cell 2017;66:22-37.e9. https://doi.org/10.1016/j.molcel.2017.02.017
  11. Yun Y, Fan X, Mao M, et al. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res 2017;27:626-41. https://doi.org/10.1038/cr.2017.31
  12. Meurens F, Summerfield A, Nauwynck H, Saif L, Gerdts V. The pig: a model for human infectious diseases. Trends Microbiol 2012;20:50-7. https://doi.org/10.1016/j.tim.2011.11.002
  13. Wu T, Zhang Z, Yuan Z, et al. Distinctive genes determine different intramuscular fat and muscle fiber ratios of the longissimus dorsi muscles in Jinhua and Landrace pigs. Plos One 2013;8:e53181. https://doi.org/10.1371/journal.pone.0053181
  14. Chen P, Baas TJ, Mabry JW, Koehler KJ. Genetic correlations between lean growth and litter traits in U.S. Yorkshire, Duroc, Hampshire, and Landrace pigs. J Anim Sci 2003;81:1700-5. https://doi.org/10.2527/2003.8171700x
  15. Jes-Niels B, Nicolas J, Heumuller AW, et al. Identification and characterization of hypoxia-regulated endothelial circular RNA. Circ Res 2015;117:884-90. https://doi.org/10.1161/CIRCRESAHA.115.306319
  16. Zheng Q, Bao C, Guo W, et al. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nat Commun 2016;7:11215. https://doi.org/10.1038/ncomms11215
  17. Mao X, Cai T, Olyarchuk JG, Wei L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 2005;21:3787-93. https://doi.org/10.1093/bioinformatics/bti430
  18. Consortium TR. RNAcentral: an international database of ncRNA sequences. Nucleic Acids Res 2015;43:D123-9. https://doi.org/10.1093/nar/gku991
  19. Zhang, XiaoOu, Wang, et al. Complementary sequencemediated exon circularization. Cell 2014;159:134-47. https://doi.org/10.1016/j.cell.2014.09.001
  20. Spurlock ME, Gabler NK. The development of porcine models of obesity and the metabolic syndrome. J Nutr 2008;138:397-402. https://doi.org/10.1093/jn/138.2.397
  21. Kim YC, Ntambi JM. Regulation of stearoyl-CoA desaturase genes: role in cellular metabolism and preadipocyte differentiation. Biochem Biophys Res Commun 1999;266:1-4. https://doi.org/10.1006/bbrc.1999.1704
  22. Treutlein J, Cichon S, Ridinger M, et al. Genome-wide association study of alcohol dependence. Arch Gen Psychiatry 2009;66:773-84. https://doi.org/10.1001/archgenpsychiatry.2009.83
  23. Li Q, Tao Z, Shi L, et al. Expression and genome polymorphism of ACSL1 gene in different pig breeds. Mol Biol Rep 2012;39: 8787-92. https://doi.org/10.1007/s11033-012-1741-6
  24. Ramos-Valdivia AC, van der Heijden R, Verpoorte R. Isopentenyl diphosphate isomerase: a core enzyme in isoprenoid biosynthesis. A review of its biochemistry and function. Nat Prod Rep 1997;14:591-603. https://doi.org/10.1039/np9971400591
  25. Romanelli MG, Lorenzi P, Sangalli A, Diani E, Mottes M. Characterization and functional analysis of cis-acting elements of the human farnesyl diphosphate synthetase (FDPS) gene 5′ flanking region. Genomics 2009;93:227-34. https://doi.org/10.1016/j.ygeno.2008.11.002
  26. Hafner M, Rezen T, Rozman D. Regulation of hepatic cytochromes p450 by lipids and cholesterol. Curr Drug Metab 2011;12: 173-85. https://doi.org/10.2174/138920011795016890
  27. Filipowicz W, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 2008;9:102-14. https://doi.org/10.1038/nrg2290
  28. Boesch-Saadatmandi C, Wagner AE, Wolffram S, Rimbach G. Effect of quercetin on inflammatory gene expression in mice liver in vivo - role of redox factor 1, miRNA-122 and miRNA- 125b. Pharmacol Res 2012;65:523-30. https://doi.org/10.1016/j.phrs.2012.02.007
  29. Huang R, Zhang Y, Han B, et al. Circular RNA HIPK2 regulates astrocyte activation via cooperation of autophagy and ER stress by targeting MIR124-2HG. Autophagy 2017;13:1722-41. https://doi.org/10.1080/15548627.2017.1356975
  30. Esau C, Davis S, Murray SF, et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab 2006;3:87-98. https://doi.org/10.1016/j.cmet.2006.01.005

Acknowledgement

Supported by : National Natural Science Foundation of China