Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage

  1. Christine A. Wells1,
  2. Timothy Ravasi1,
  3. Razvan Sultana2,
  4. Ken Yagi3,
  5. Piero Carninci3,
  6. Hidemasa Bono3,
  7. Geoffrey Faulkner1,
  8. Yasushi Okazaki3,
  9. John Quackenbush2,
  10. David A. Hume1,
  11. RIKEN GER Group3,
  12. GSL Members4,7, and
  13. Paul A. Lyons5,6
  1. 1Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
  2. 2The Institute for Genomic Research, Rockville, Maryland 20850, USA
  3. 3Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
  4. 4Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan
  5. 5JDRF/WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom

Abstract

The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the present study we have assessed the complexity of the transcriptome expressed in mouse macrophages before and after treatment with lipopolysaccharide, a global regulator of macrophage gene expression, using existing RIKEN 19K arrays. By comparison to array profiles of other cells and tissues, we identify a large set of macrophage-enriched genes, many of which have obvious functions in endocytosis and phagocytosis. In addition, a significant number of LPS-inducible genes were identified. The data suggest that macrophages are a complex source of mRNA for transcriptome studies. To assess complexity and identify additional macrophage expressed genes, cDNA libraries were created from purified populations of macrophage and dendritic cells, a functionally related cell type. Sequence analysis revealed a high incidence of novel mRNAs within these cDNA libraries. These studies provide insights into the depths of transcriptional complexity still untapped amongst products of inducible genes, and identify macrophage and dendritic cell populations as a starting point for sampling the inducible mammalian transcriptome.

Footnotes

  • [Supplemental material is available online at www.genome.org.] The sequence data from this study have been submitted to DDBT under accession nos. AK089166–AK089912, BY153905–BY223868, BY681767–BY576025, BY742706–BY765561, BY767554–BY752495, BY761159–BY761576, and BY763617–BY766105. The expression data from this study have been submitted to GEO under accession nos. GPL256, GSM4635–GSM4669, and GSE324–GSE326.

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1056103.

  • ↵7 Takahiro Arakawa, Jun Kawai, and Yoshihide Hayashizaki.

  • ↵6 Corresponding author. E-MAIL paul.lyons{at}cimr.cam.ac.uk; FAX 1223-762102.

    • Accepted February 25, 2003.
    • Received December 11, 2002.
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  1. doi: 10.1101/gr.1056103 Genome Res. 13: 1360-1365 Cold Spring Harbor Laboratory Press

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