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Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing

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Abstract

Microarray analysis has made it feasible to carry out extensive gene expression profiling in a single assay. Various hematopoietic stem cell (HSC) populations have been subjected to microarray analyses and their profiles of gene expression have been reported. However, this approach is not suitable to identify novel transcripts or for profiling of genes with low expression levels. To obtain a detailed gene expression profile of CD34−c-Kit+Sca-1+lineage marker-negative (Lin−) (CD34−KSL) HSCs, we constructed a CD34−KSL cDNA library, performed high-throughput sequencing, and compared the generated profile with that of another HSC fraction, side population (SP) Lin− (SP Lin−) cells. Sequencing of the 5′-termini of about 9,500 cDNAs from each HSC library identified 1,424 and 2,078 different genes from the CD34−KSL and SP Lin− libraries, respectively. To exclude ubiquitously expressed genes including housekeeping genes, digital subtraction was successfully performed against EST databases of other organs, leaving 25 HSC-specific genes including five novel genes. Among 4,450 transcripts from the CD34−KSL cDNA library that showed no homology to the presumable protein-coding genes, 29 were identified as strong candidates for mRNA-like non-coding RNAs by in silico analyses. Our cyclopedic approaches may contribute to understanding of novel molecular aspects of HSC function.

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Author information

Author notes

  1. Atsushi Iwama

    Present address: Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan

  2. Tomohide Yabiku

    Present address: Interdisciplinary Intelligent Systems Engineering Course, Graduate School of Engineering and Science, Ryukyu University, Okinawa, 903-0213, Japan

  3. Takashi Minowa

    Present address: Nanotechnology Innovation Center, National Institute for Materials Science, Ibaraki, 305-0047, Japan

  4. Mitsujiro Osawa

    Present address: Department of Developmental Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9133, USA

Authors and Affiliations

  1. Division of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan

    Yoshimi Yashiro, Mitsujiro Osawa, Atsushi Iwama & Hiromitsu Nakauchi

  2. Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan

    Hideo Bannai, Tomohide Yabiku & Satoru Miyano

  3. Department of Informatics, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan

    Hideo Bannai

  4. Hitachi, Ltd, Life Science Group, Saitama, 350-1165, Japan

    Takashi Minowa

  5. Laboratory of Stem Cell Therapy, Center for Experimental Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan

    Hiromitsu Nakauchi

Authors
  1. Yoshimi Yashiro
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  2. Hideo Bannai
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  3. Takashi Minowa
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  4. Tomohide Yabiku
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  5. Satoru Miyano
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  6. Mitsujiro Osawa
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  7. Atsushi Iwama
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  8. Hiromitsu Nakauchi
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Corresponding author

Correspondence to Hiromitsu Nakauchi.

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Yashiro, Y., Bannai, H., Minowa, T. et al. Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing. Int J Hematol 89, 24–33 (2009). https://doi.org/10.1007/s12185-008-0212-2

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  • DOI: https://doi.org/10.1007/s12185-008-0212-2

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