Cited by 216Genomics and Phylogenetic StudiesTuberculosis Research and EpidemiologyGene expression and cancer classification

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Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

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Hegedűs, Zoltán, Zakrzewska, Anna, Ágoston, Vilmos C., Ordas, Anita, Rácz, Péter, Mink, Mátyás, Spaink, Herman P., Meijer, Annemarie H.·2009·Molecular Immunology

DOI 10.1016/j.molimm.2009.07.002

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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.

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Self-citation

Authors: Hegedűs, Z., Zakrzewska, A., Ágoston, V. C., Ordas, A., Rácz, P., Mink, M., Spaink, H. P., & Meijer, A. H.
Affiliations: Leiden University (NL)
University of Szeged (HU)
Corresponding author: Meijer, Annemarie H.
ORCID: Ordas, Anita
Mink, Mátyás
Spaink, Herman P.
Meijer, Annemarie H.
Venue: Molecular Immunology
Publisher: Elsevier BV
Published: 2009-09
Volume: 46
Issue: 15
Pages: 2918-2930
ISSN: 0161-5890 (ISSN-L)
DOI: 10.1016/j.molimm.2009.07.002
OpenAlex: W1966486838
Cited by: 216
References: 58
Citations by year: 2025: 2 · 2024: 1 · 2023: 4 · 2022: 1 · 2021: 6 · 2020: 13 · 2019: 16 · 2018: 5 · 2017: 6 · 2016: 15 · 2015: 19 · 2014: 26 · 2013: 25 · 2012: 30
FWCI: 10.29
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Molecular Immunology (publishedVersion)
PubMed (publishedVersion)
Leiden Repository (Leiden University) (submittedVersion)
Funders: European Commission
Universiteit Leiden
Leids Universitair Medisch Centrum
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Keywords: zebrafish, mycobacterial infection, transcriptome, digital gene expression, gene expression profiling, alternative splicing, isoform switching, novel transcripts, microarray comparison
MeSH terms: Animals, Disease Models, Animal, Humans, Male, Mycobacterium Infections, Zebrafish, Transcriptional Activation, Sequence Analysis, RNA, Mycobacterium marinum, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Host-Pathogen Interactions

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Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

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