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Letter

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

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 ²The Institute for Genomic Research, Rockville, Maryland 20850, USA ³Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan ⁴Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan ⁵JDRF/WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom

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.

⁷ Takahiro Arakawa, Jun Kawai, and Yoshihide Hayashizaki.

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

[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.

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