Abstract
Gene expression profiles of hematopoietic stem cells (HSCs) provide clues for understanding molecular mechanisms of HSC behavior, including self-renewal and differentiation. We took advantage of serial analysis of gene expression (SAGE) to identify medium- and low-abundant transcripts expressed in HSCs/hematopoietic progenitor cells (HPCs). Among a total of 31,380 unique transcripts, 17,326 (55%) correspond to known genes and, 14,054 (45%) are low-copy transcripts that have no matches to currently known genes. Among the former class, 3,899 (23%) were alternatively spliced transcripts and 3,754 (22%) represent anti-sense transcripts from known genes. Mapping of the SAGE tags to the mouse genome showed that differences in gene expression exist among chromosomes. In addition, comparison of the HSCs/HPCs SAGE data to that of myeloid progenitor cells revealed that massive genetic reprogramming occurs in hematopoietic cell differentiation. Our results demonstrate a previously unrecognized complexity of gene expression in HSCs/HPCs, and indicate the need for further efforts to fully identify and characterize the transcripts expressed in this cell type.
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Acknowledgments
This work was supported by the SRC Program of the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korea Government (2009-0063409) and WCU (World Class University) Program through the Korea Science and Engineering Foundation funded by the Ministry of Education, Science and Technology (R33-2008-000-10070-0).
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Communicated by P. Ruiz.
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Kim, HS., Hwang, J., Kim, YH. et al. Detection of low-abundant novel transcripts in mouse hematopoietic stem cells. Mol Genet Genomics 282, 363–370 (2009). https://doi.org/10.1007/s00438-009-0469-z
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DOI: https://doi.org/10.1007/s00438-009-0469-z