RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish

BMC Genomics. 2012 Jul 17;13:319. doi: 10.1186/1471-2164-13-319.


Background: Zebrafish (Danio rerio) is a prominent vertebrate model of human development and pathogenic disease and has recently been utilized to study teleost immune responses to infectious agents threatening the aquaculture industry. In this work, to clarify the host immune mechanisms underlying the protective effects of a putative vaccine and improve its immunogenicity in the future efforts, high-throughput RNA sequencing technology was used to investigate the immunization-related gene expression patterns of zebrafish immunized with Edwardsiella tarda live attenuated vaccine.

Results: Average reads of 18.13 million and 14.27 million were obtained from livers of zebrafish immunized with phosphate buffered saline (mock) and E. tarda vaccine (WED), respectively. The reads were annotated with the Ensembl zebrafish database before differential expressed genes sequencing (DESeq) comparative analysis, which identified 4565 significantly differentially expressed genes (2186 up-regulated and 2379 down-regulated in WED; p<0.05). Among those, functional classifications were found in the Gene Ontology database for 3891 and in the Kyoto Encyclopedia of Genes and Genomes database for 3467. Several pathways involved in acute phase response, complement activation, immune/defense response, and antigen processing and presentation were remarkably affected at the early stage of WED immunization. Further qPCR analysis confirmed that the genes encoding the factors involved in major histocompatibility complex (MHC)-I processing pathway were up-regulated, while those involved in MHC-II pathway were down-regulated.

Conclusion: These data provided insights into the molecular mechanisms underlying zebrafish immune response to WED immunization and might aid future studies to develop a highly immunogenic vaccine against gram-negative bacteria in teleosts.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacterial Vaccines / immunology
  • Databases, Genetic
  • Edwardsiella tarda / immunology
  • Edwardsiella tarda / metabolism
  • Gene Expression Profiling*
  • Genes, MHC Class I / genetics*
  • Genes, MHC Class II / genetics*
  • Immunization
  • Liver / metabolism*
  • RNA / chemistry
  • RNA / metabolism*
  • Sequence Analysis, RNA
  • Signal Transduction / genetics
  • Toll-Like Receptors / metabolism
  • Zebrafish / genetics
  • Zebrafish / immunology
  • Zebrafish / metabolism


  • Bacterial Vaccines
  • Toll-Like Receptors
  • RNA