Original Article

International Journal of Hematology

, Volume 89, Issue 1, pp 24-33

Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing

  • Yoshimi YashiroAffiliated withDivision of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical Science, University of Tokyo
  • , Hideo BannaiAffiliated withLaboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of TokyoDepartment of Informatics, Kyushu University
  • , Takashi MinowaAffiliated withHitachi, Ltd, Life Science GroupNanotechnology Innovation Center, National Institute for Materials Science
  • , Tomohide YabikuAffiliated withLaboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of TokyoInterdisciplinary Intelligent Systems Engineering Course, Graduate School of Engineering and Science, Ryukyu University
  • , Satoru MiyanoAffiliated withLaboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo
  • , Mitsujiro OsawaAffiliated withDivision of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical Science, University of TokyoDepartment of Developmental Biology, University of Texas Southwestern Medical Center
  • , Atsushi IwamaAffiliated withDivision of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical Science, University of TokyoDepartment of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University
  • , Hiromitsu NakauchiAffiliated withDivision of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical Science, University of TokyoLaboratory of Stem Cell Therapy, Center for Experimental Medicine, The Institute of Medical Science, University of Tokyo Email author 

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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 CD34c-Kit+Sca-1+lineage marker-negative (Lin) (CD34KSL) HSCs, we constructed a CD34KSL 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 CD34KSL 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 CD34KSL 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.

Keywords

Hematopoietic stem cells High-throughput sequencing Non-coding RNA