Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing

Yoshimi Yashiro, Hideo Bannai, Takashi Minowa, Tomohide Yabiku, Satoru Miyano, Mitsujiro Osawa, Atsushi Iwama, Hiromitsu Nakauchi

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)24-33
Number of pages10
JournalInternational journal of hematology
Volume89
Issue number1
DOIs
Publication statusPublished - Jan 1 2009

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Hematopoietic Stem Cells
Genes
Microarray Analysis
Gene Library
Transcriptome
Side-Population Cells
Untranslated RNA
Essential Genes
Expressed Sequence Tags
Gene Expression Profiling
Computer Simulation
Population
Libraries
Complementary DNA
Databases
Messenger RNA
Proteins

All Science Journal Classification (ASJC) codes

  • Hematology

Cite this

Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing. / Yashiro, Yoshimi; Bannai, Hideo; Minowa, Takashi; Yabiku, Tomohide; Miyano, Satoru; Osawa, Mitsujiro; Iwama, Atsushi; Nakauchi, Hiromitsu.

In: International journal of hematology, Vol. 89, No. 1, 01.01.2009, p. 24-33.

Research output: Contribution to journalArticle

Yashiro, Y, Bannai, H, Minowa, T, Yabiku, T, Miyano, S, Osawa, M, Iwama, A & Nakauchi, H 2009, 'Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing', International journal of hematology, vol. 89, no. 1, pp. 24-33. https://doi.org/10.1007/s12185-008-0212-2
Yashiro, Yoshimi ; Bannai, Hideo ; Minowa, Takashi ; Yabiku, Tomohide ; Miyano, Satoru ; Osawa, Mitsujiro ; Iwama, Atsushi ; Nakauchi, Hiromitsu. / Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing. In: International journal of hematology. 2009 ; Vol. 89, No. 1. pp. 24-33.
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