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Functional & integrative genomics
Sep, 2019;19 (5): 775-786.

High-throughput sequencing reveals microRNAs in response to heat stress in the head kidney of rainbow trout (Oncorhynchus mykiss).

Fang Ma, Zhe Liu, Jinqiang Huang, Yongjuan Li, Yujun Kang, Xiaoxia Liu, Jianfu Wang
Author Information
  1. Fang Ma: College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
  2. Zhe Liu: College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China. liuz@gsau.edu.cn. ORCID
  3. Jinqiang Huang: College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
  4. Yongjuan Li: College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
  5. Yujun Kang: College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
  6. Xiaoxia Liu: College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
  7. Jianfu Wang: College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
PMID: 31076931 DOI: 10.1007/s10142-019-00682-3

Abstract

Recently, the research of animal microRNAs (miRNAs) has attracted wide attention for its regulatory effect in the development process and the response to abiotic stresses. Rainbow trout is a commercially and cold water fish species, and usually encounters heat stress, which affects its growth and leads to a huge economic loss. But there were few investigations about the roles of miRNAs in heat stress in rainbow trout. In this study, miRNAs of rainbow trout which were involved in heat stress were identified by high-throughput sequencing of six small RNA libraries from head kidney tissues under control (18 °C) and heat-treated (24 °C) conditions. A total of 392 conserved miRNAs and 989 novel miRNAs were identified, of which 78 miRNAs were expressed in different response to heat stress. Ten of these miRNAs were further validated by quantitative real-time PCR. In addition to, including 393 negative correlation miRNA-target gene pairs, several important regulatory pathways were involved in heat stress of the potential target genes, including protein processing in endoplasmic reticulum, NOD-like receptor signaling pathway, and phagosome. Our data significantly advance understanding of heat stress regulatory mechanism of miRNA in the head kidney of rainbow trout, which provide a useful resource for the cultivation of rainbow trout.

Keywords

Heat stress High-throughput sequencing Rainbow trout miRNA

References

  1. Am J Physiol. 1999 Apr;276(4):R990-6 [PMID: 10198376]
  2. Nature. 2000 Feb 24;403(6772):901-6 [PMID: 10706289]
  3. Mar Biotechnol (NY). 2000 Jul;2(4):329-338 [PMID: 10960122]
  4. Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10716-21 [PMID: 11535826]
  5. Methods. 2001 Dec;25(4):402-8 [PMID: 11846609]
  6. Comp Biochem Physiol C Toxicol Pharmacol. 2002 Jun;132(2):223-33 [PMID: 12106899]
  7. Cell. 2004 Jan 23;116(2):281-97 [PMID: 14744438]
  8. Nat Rev Genet. 2004 Jul;5(7):522-31 [PMID: 15211354]
  9. Physiol Behav. 2004 Dec 15;83(3):373-6 [PMID: 15581658]
  10. Biochim Biophys Acta. 2005 Jan 11;1681(2-3):99-106 [PMID: 15627501]
  11. Biochem Biophys Res Commun. 2005 Apr 1;329(1):51-7 [PMID: 15721272]
  12. Nature. 2005 Mar 17;434(7031):338-45 [PMID: 15735639]
  13. Cell Mol Life Sci. 2005 Mar;62(6):670-84 [PMID: 15770419]
  14. Bioinformatics. 2005 Oct 1;21(19):3787-93 [PMID: 15817693]
  15. Drug Discov Today. 2005 Apr 15;10(8):595-601 [PMID: 15837603]
  16. Plant Cell. 2005 Jun;17(6):1658-73 [PMID: 15849273]
  17. Genes Dev. 2005 Jun 1;19(11):1288-93 [PMID: 15937218]
  18. Nat Genet. 2005 Jul;37(7):766-70 [PMID: 15965474]
  19. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii93-100 [PMID: 16204133]
  20. Comp Biochem Physiol B Biochem Mol Biol. 2005 Dec;142(4):426-31 [PMID: 16257553]
  21. Mol Cell Biol. 2005 Nov;25(22):9793-805 [PMID: 16260597]
  22. Nat Genet. 2006 Dec;38(12):1375-7 [PMID: 17072315]
  23. J Cell Physiol. 2007 Feb;210(2):279-89 [PMID: 17096367]
  24. Trends Cell Biol. 2007 Mar;17(3):118-26 [PMID: 17197185]
  25. Ecotoxicol Environ Saf. 2007 Sep;68(1):13-9 [PMID: 17257677]
  26. Cell. 2007 Apr 6;129(1):147-61 [PMID: 17382377]
  27. Science. 2007 Apr 27;316(5824):604-8 [PMID: 17463289]
  28. Annu Rev Cell Dev Biol. 2007;23:175-205 [PMID: 17506695]
  29. Comp Biochem Physiol B Biochem Mol Biol. 2007 Nov;148(3):277-85 [PMID: 17644445]
  30. Comp Biochem Physiol B Biochem Mol Biol. 2008 Apr;149(4):552-6 [PMID: 18234536]
  31. BMC Dev Biol. 2008 Apr 15;8:41 [PMID: 18412968]
  32. BMC Genomics. 2008 May 29;9:253 [PMID: 18510755]
  33. PLoS One. 2008 Jul 30;3(7):e2818 [PMID: 18665242]
  34. Cell Stress Chaperones. 2009 Mar;14(2):161-72 [PMID: 18668349]
  35. Genome Biol. 2009;10(3):R25 [PMID: 19261174]
  36. Mar Biotechnol (NY). 2010 Aug;12(4):410-29 [PMID: 19816740]
  37. Proc Biol Sci. 2010 Mar 22;277(1683):905-13 [PMID: 19923129]
  38. BMC Genomics. 2010 Jan 28;11:72 [PMID: 20109224]
  39. Genome Biol. 2010;11(2):R14 [PMID: 20132535]
  40. Am J Physiol Regul Integr Comp Physiol. 2010 Sep;299(3):R843-52 [PMID: 20610827]
  41. PLoS One. 2010 Dec 30;5(12):e15224 [PMID: 21253009]
  42. J Biomed Sci. 2011 Mar 16;18:22 [PMID: 21406115]
  43. BMC Genomics. 2011 Apr 07;12:180 [PMID: 21473775]
  44. PLoS One. 2011;6(5):e19523 [PMID: 21603611]
  45. Biochim Biophys Acta. 2012 Feb;1819(2):137-48 [PMID: 21605713]
  46. J Fish Dis. 2011 Aug;34(8):619-27 [PMID: 21762173]
  47. Am J Physiol Regul Integr Comp Physiol. 2011 Nov;301(5):R1453-66 [PMID: 21865546]
  48. Nucleic Acids Res. 2012 Jan;40(1):37-52 [PMID: 21911355]
  49. J Immunol. 2011 Dec 15;187(12):6171-5 [PMID: 22084432]
  50. BMC Genomics. 2011 Dec 14;12:605 [PMID: 22168751]
  51. PLoS One. 2012;7(3):e33040 [PMID: 22479356]
  52. Mol Genet Genomics. 2012 Jul;287(7):555-63 [PMID: 22643909]
  53. J Plant Physiol. 2012 Nov 1;169(16):1664-72 [PMID: 22647959]
  54. PLoS One. 2012;7(5):e37209 [PMID: 22666345]
  55. BMC Bioinformatics. 2012 Jun 21;13:140 [PMID: 22720726]
  56. Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):14247-52 [PMID: 22891320]
  57. Hum Genomics. 2012 Jul 05;6:6 [PMID: 23245351]
  58. Fish Shellfish Immunol. 2013 Aug;35(2):429-37 [PMID: 23684810]
  59. BMC Genomics. 2013 Jul 17;14:482 [PMID: 23865519]
  60. Nucleic Acids Res. 2014 Jan;42(Database issue):D68-73 [PMID: 24275495]
  61. BMC Genomics. 2014 Mar 27;15:242 [PMID: 24673837]
  62. BMC Genomics. 2014 Jun 25;15:525 [PMID: 24966054]
  63. Microrna. 2012;1(1):1 [PMID: 25048083]
  64. Genome Biol Evol. 2014 Jul 22;6(8):1911-37 [PMID: 25053657]
  65. PLoS One. 2014 Oct 03;9(10):e108582 [PMID: 25279944]
  66. PLoS One. 2014 Oct 28;9(10):e110698 [PMID: 25350659]
  67. Sci Rep. 2015 Mar 09;5:8866 [PMID: 25746291]
  68. Genet Mol Res. 2015 May 18;14(2):5280-6 [PMID: 26125723]
  69. FASEB J. 2015 Dec;29(12):4901-13 [PMID: 26265472]
  70. Gene. 2016 Jan 10;575(2 Pt 1):171-86 [PMID: 26358502]
  71. Zebrafish. 2015 Dec;12(6):387-97 [PMID: 26418264]
  72. Fish Physiol Biochem. 2016 Apr;42(2):701-10 [PMID: 26614500]
  73. BMC Genomics. 2016 Mar 01;17:164 [PMID: 26931235]
  74. Sci Rep. 2016 Mar 04;6:22687 [PMID: 26940974]
  75. Gene. 2016 Aug 10;587(2):155-62 [PMID: 27154818]
  76. Arch Toxicol. 2017 Feb;91(2):921-933 [PMID: 27339418]
  77. Chemosphere. 2017 Jan;166:445-452 [PMID: 27705832]
  78. Gene. 2017 Jul 1;619:1-9 [PMID: 28365313]
  79. J Dig Dis. 2017 Jun;18(6):330-342 [PMID: 28509372]
  80. Sci Rep. 2017 Aug 18;7(1):8705 [PMID: 28821885]
  81. Funct Integr Genomics. 2018 Jan;18(1):67-78 [PMID: 28956210]
  82. PLoS One. 2017 Oct 18;12(10):e0186433 [PMID: 29045433]
  83. Funct Integr Genomics. 2018 Nov;18(6):645-657 [PMID: 29948458]
  84. Funct Integr Genomics. 2019 Mar;19(2):265-280 [PMID: 30443850]
  85. Cell. 1993 Dec 3;75(5):843-54 [PMID: 8252621]

Grants

  1. 31660735/National Natural Science Foundation of China

MeSH Term

Animals
Gene Expression Regulation
Head Kidney
Heat-Shock Response
High-Throughput Nucleotide Sequencing
MicroRNAs
Oncorhynchus mykiss
Signal Transduction
Stress, Physiological
Transcriptome

Chemicals

MicroRNAs
Journal Article

Word Cloud

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