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Non-coding RNAs revealed during identification of genes involved in chicken immune responses

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Abstract

Recent large-scale cDNA cloning studies have shown that a significant proportion of the transcripts expressed from vertebrate genomes do not appear to encode protein. Moreover, it was reported in mammals (human and mice) that these non-coding transcripts are expressed and regulated by mechanisms similar to those involved in the control of protein-coding genes. We have produced a collection of cDNA sequences from immunologically active tissues with the aim of discovering chicken genes involved in immune mechanisms, and we decided to explore the non-coding component of these immune-related libraries. After finding known non-coding RNAs (miRNA, snRNA, snoRNA), we identified new putative mRNA-like non-coding RNAs. We characterised their expression profiles in immune-related samples. Some of them showed changes in expression following viral infections. As they exhibit patterns of expression that parallel the behaviour of protein-coding RNAs in immune tissues, our study suggests that they could play an active role in the immune response.

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Acknowledgements

This research was supported by funds from the European Commission to RZ (KA5-QLRT-CT99-1591 Chicken IMAGE). T.R. was supported by grants from the SABRE Integrated European project (FOOD-CT-2006-016250), and M.E.A. by grants from the French Ministere de la Recherche. We thank Dr F. Dautry for helpful discussion.

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Authors and Affiliations

  1. CNRS, FRE2937, 7 rue Guy Moquet, F-94800, Villejuif, France

    Marie-Laure Endale Ahanda, Thomas Ruby, Veronique Morin, Anne Oudin & Rima Zoorob

  2. Botanical museum (LD), Lund University, Ostra Vallgata 18, Lund, Sweden

    Håkan Wittzell

  3. INRA/AgroParisTech, UMR1236, Génétique et Diversité Animales, F-78352, Jouy-en-Josas, France

    Bertrand Bed’Hom

  4. INRA, UR1282 Infectiologie Animale et Santé Publique, F-37380, Nouzilly, France

    Anne-Marie Chaussé

  5. INSERM IFR026, Plateforme Transcriptome Ouest Génopole, Nantes, France

    Catherine Chevalier

  6. Institute for Animal Health, Compton, Berkshire, RG20 7NN, UK

    John R. Young

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  1. Marie-Laure Endale Ahanda
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  2. Thomas Ruby
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Correspondence to Rima Zoorob.

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Additional data file 1

Table of putative ncRNAs associated data including localisation, comparison with previous study and expression information (XLS 52 kb)

Additional data file 2

Dendrograms of the 15 clusters obtained by k-mean clustering of both coding and non-coding transcripts based on expression levels from immune-related tissues (GIF 5841 kb)

High resolution image file (EPS 16775 kb)

Additional data file 3

Descriptions of the transcripts included in each expression cluster of the immune-related tissues analysis (TXT 138 kb)

Additional data file 4

Dendrograms of the 15 clusters obtained by k-mean clustering of both coding and non-coding transcripts based on expression levels from the IBDV infection (GIF 2032 kb)

High resolution image file (EPS 7938 kb)

Additional data file 5

Descriptions of the transcripts included in each expression cluster of the IBDV infection analysis (TXT 114 kb)

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Ahanda, ML.E., Ruby, T., Wittzell, H. et al. Non-coding RNAs revealed during identification of genes involved in chicken immune responses. Immunogenetics 61, 55–70 (2009). https://doi.org/10.1007/s00251-008-0337-8

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  • DOI: https://doi.org/10.1007/s00251-008-0337-8

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