Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing.
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.
Yashiro
Yoshimi
Y
Division of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
Bannai
Hideo
H
Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.|Department of Informatics, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.
Minowa
Takashi
T
Hitachi, Ltd, Life Science Group, Saitama, 350-1165, Japan.|Nanotechnology Innovation Center, National Institute for Materials Science, Ibaraki, 305-0047, Japan.
Yabiku
Tomohide
T
Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.|Interdisciplinary Intelligent Systems Engineering Course, Graduate School of Engineering and Science, Ryukyu University, Okinawa, 903-0213, Japan.
Miyano
Satoru
S
Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
Osawa
Mitsujiro
M
Division of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.|Department of Developmental Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9133, USA.
Iwama
Atsushi
A
Division of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.|Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan.
Nakauchi
Hiromitsu
H
Division of Stem Cell Therapy, Center for Stem Cell and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan. nakauchi@ims.u-tokyo.ac.jp.|Laboratory of Stem Cell Therapy, Center for Experimental Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan. nakauchi@ims.u-tokyo.ac.jp.
D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D023281:Genomics / Q000379:methods; D006412:Hematopoietic Stem Cells; D006801:Humans; D017422:Sequence Analysis, DNA