Display Settings:

Format

Send to:

Choose Destination
We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Mol Immunol. 2009 Sep;46(15):2918-30. doi: 10.1016/j.molimm.2009.07.002. Epub 2009 Jul 24.

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection.

Author information

  • 1Zenon Bio Ltd., Maros u. 40, H-6721 Szeged, Hungary.

Abstract

Novel high-throughput deep sequencing technology has dramatically changed the way that the functional complexity of transcriptomes can be studied. Here we report on the first use of this technology to gain insight into the wide range of transcriptional responses that are associated with an infectious disease process. Using Solexa/Illumina's digital gene expression (DGE) system, a tag-based transcriptome sequencing method, we investigated mycobacterium-induced transcriptome changes in a model vertebrate species, the zebrafish. We obtained a sequencing depth of over 5 million tags per sample with strong correlation between replicates. Tag mapping indicated that healthy and infected adult zebrafish express over 70% of all genes represented in transcript databases. Comparison of the data with a previous multi-platform microarray analysis showed that both types of technologies identified regulation of similar functional groups of genes. However, the unbiased nature of DGE analysis provided insights that microarray analysis could not have achieved. In particular, we show that DGE data sets are instrumental for verification of predicted gene models and allowed us to detect mycobacterium-regulated switching between different transcript isoforms. Moreover, genomic mapping of infection-induced DGE tags revealed novel transcript forms for which any previous EST-based evidence of expression was lacking. In conclusion, our deep sequencing analysis revealed in depth the high degree of transcriptional complexity of the host response to mycobacterial infection and resulted in the discovery and validation of new gene products with induced expression in infected individuals.

PMID:
19631987
[PubMed - indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Elsevier Science
    Loading ...
    Write to the Help Desk