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Identification of novel genes and transcription factors involved in spleen, thymus and immunological development and function

Genes & Immunity volume 7, pages 101–112 (2006)Cite this article

Abstract

We constructed and analyzed six serial analysis of gene expression (SAGE) libraries to identify genes with previously uncharacterized roles in spleen or thymus development. A total of 625 070 tags were sequenced from the three spleen (embryonic day (E)15.5, E16.5 and adult) and three thymus (E15.5, E18.5 and adult) libraries. These tags corresponded to 83 182 tag types, which mapped unambiguously to 36 133 different genes. Genes over-represented in these libraries, compared to 115 mouse SAGE libraries (www.mouseatlas.org), included genes of known and unknown immunological or developmental relevance. The expression profiles of 11 genes with unknown roles in spleen and thymus development were validated using reverse transcription-qPCR. We further characterized the expression of one of these candidates, RIKEN cDNA 9230105E10 that encodes a murine homolog of Trim5α, in numerous adult tissues and immune cell types. In addition, we demonstrate that transcript levels are upregulated in response to TLR stimulation of plasmacytoid dendritic cells and macrophages. This work provides the first evidence of regulated and cell type-specific expression of this gene. In addition, these observations suggest that the SAGE libraries provide an important resource for further investigations into the molecular mechanisms regulating spleen and thymus organogenesis, as well as the development of immunological competence.

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Acknowledgements

Eosinophil and mast cell RNA was a kind gift from BH Koller, CD25− and Treg cell RNA were a kind gift from J Serody and purified B cells were a kind gift of SH Clarke. This work was carried out as part of the Mouse Atlas of Gene Expression Project, a collaborative project involving the following Principle Investigators: Cheryl D Helgason, Pamela Hoodless, Steven Jones, Marco Marra, Elizabeth M Simpson and Greg Riggins. Daniella Gerhardt and Robert Strausberg were also important contributors to this project. We would like to acknowledge members of the Genome Sciences Center sequencing, bioinformatics and SAGE library construction teams, in particular Anita Charters, Jennifer Asano, Allen Delaney, Jaswinder Khattra and Asim Siddiqui, for their valuable contributions. We would also like to thank Adrian Burke and Caroline Astell for their assistance in project management and the staff of the Joint Animal Facility at the BBCRC for maintaining the mice. Funding for this project was provided by Genome Canada through Genome BC (CDH) and the National Institute of Health AI29564 (JT), with infrastructure support provided by the BC Cancer Foundation. Kristi L Williams is supported in part by the 2004 Amgen/Focis Fellowship Award, whereas Cheryl D Helgason is a scholar of the Canadian Institutes of Health Research and the Michael Smith Foundation for Health Research.

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Authors and Affiliations

  1. BC Cancer Agency, Vancouver, BC, Canada

    B G Hoffman, A H Tien, V Lu, T Ruiz de Algara & C D Helgason

  2. University of North Carolina Chapel Hill, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA

    K L Williams & Jp-y Ting

  3. Department of Surgery, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada

    C D Helgason

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  1. B G Hoffman
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Correspondence to C D Helgason.

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Hoffman, B., Williams, K., Tien, A. et al. Identification of novel genes and transcription factors involved in spleen, thymus and immunological development and function. Genes Immun 7, 101–112 (2006). https://doi.org/10.1038/sj.gene.6364270

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