Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing
First Online: 03 December 2008 Received: 19 August 2008 Revised: 01 October 2008 Accepted: 23 October 2008 DOI:
Cite this article as: Yashiro, Y., Bannai, H., Minowa, T. et al. Int J Hematol (2009) 89: 24. doi:10.1007/s12185-008-0212-2 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. Keywords Hematopoietic stem cells High-throughput sequencing Non-coding RNA Electronic supplementary material
The online version of this article (doi:
) contains supplementary material, which is available to authorized users. 10.1007/s12185-008-0212-2 References
Osawa M, Hanada K, Hamada H, Nakauchi H. Long-term lymphohematopoietic reconstitution by a single CD34-low/negative hematopoietic stem cell. Science. 1996;273:242–5.
Goodell MA, Brose K, Paradis G, Conner AS, Mulligan RC. Isolation and functional properties of murine hematopoietic stem cells that are replicating in vivo. J Exp Med. 1996;183:1797–806.
Zhou S, Schuetz JD, Bunting KD, Colapietro AM, Sampath J, Morris JJ, et al. The ABC transporter Bcrp1/ABCG2 is expressed in a wide variety of stem cells and is a molecular determinant of the side-population phenotype. Nat Med. 2001;7:1028–34.
Bertoncello I, Hodgson GS, Bradley TR. Multiparameter analysis of transplantable hemopoietic stem cells: I. The separation and enrichment of stem cells homing to marrow and spleen on the basis of rhodamine-123 fluorescence. Exp Hematol. 1985;13:999–1006.
Spangrude GJ, Heimfeld S, Weissman IL. Purification and characterization of mouse hematopoietic stem cells. Science. 1988;241:58–62.
Uchida N, Weissman IL. Searching for hematopoietic stem cells: evidence that Thy-1.1lo Lin- Sca-1+ cells are the only stem cells in C57BL/Ka-Thy-1.1 bone marrow. J Exp Med. 1992;175:175–84.
Jordan CT, Astle CM, Zawadzki J, Mackarehtschian K, Lemischka IR, Harrison DE. Long-term repopulating abilities of enriched fetal liver stem cells measured by competitive repopulation. Exp Hematol. 1995;23:1011–5.
Terskikh AV, Easterday MC, Li L, Hood L, Kornblum HI, Geschwind DH, et al. From hematopoiesis to neuropoiesis: evidence of overlapping genetic programs. Proc Natl Acad Sci USA. 2001;98:7934–9.
Park IK, He Y, Lin F, Laerum OD, Tian Q, Bumgarner R, et al. Differential gene expression profiling of adult murine hematopoietic stem cells. Blood. 2002;99:488–98.
Venezia TA, Merchant AA, Ramos CA, Whitehouse NL, Young AS, Shaw CA, et al. Molecular signatures of proliferation and quiescence in hematopoietic stem cells. PLoS Biol. 2004;2(10):e301. doi:
Phillips RL, Ernst RE, Brunk B, Ivanova N, Mahan MA, Deanehan JK, et al. The genetic program of hematopoietic stem cells. Science. 2000;288:1635–40.
Ivanova NB, Dimos JT, Schaniel C, Hackney JA, Moore KA, Lemischka IR. A stem cell molecular signature. Science. 2002;298:601–4.
Chambers SM, Boles NC, Lin KY, Tierney MP, Bowman TV, Bradfute SB, et al. Hematopoietic fingerprints: an expression database of stem cells and their progeny. Cell Stem Cell. 2007;1:578–91.
Kitamura T, Koshino Y, Shibata F, Oki T, Nakajima H, Nosaka T, et al. Retrovirus-mediated gene transfer and expression cloning: powerful tools in functional genomics. Exp Hematol. 2003;31:1007–14.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000;25:25–9.
Osawa M, Yamaguchi T, Nakamura Y, Kaneko S, Onodera M, Sawada K, et al. Erythroid expansion mediated by the Gfi-1B zinc finger protein: role in normal hematopoiesis. Blood. 2002;100:2769–77.
Chen CZ, Li L, Lodish HF, Bartel DP. MicroRNAs modulate hematopoietic lineage differentiation. Science. 2004;303:83–6.
Wagner LA, Christensen CJ, Dunn DM, Spangrude GJ, Georgelas A, Kelley L, et al. EGO, a novel, noncoding RNA gene, regulates eosinophil granule protein transcript expression. Blood. 2007;109:5191–8.
Akashi K, He X, Chen J, Iwasaki H, Niu C, Steenhard B, et al. Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis. Blood. 2003;101:383–9.
Ramalho-Santos M, Yoon S, Matsuzaki Y, Mulligan RC, Melton DA. “Stemness”: transcriptional profiling of embryonic and adult stem cells. Science. 2002;298:597–600.
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, et al. Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs. Nature. 2002;420:563–73.
Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming KG, et al. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res. 2003;13:1301–6.
Simin K, Scuderi A, Reamey J, Dunn S, Weiss R, Metherall JE, et al. Profiling patterned transcripts in Drosophila embryos. Genome Res. 2002;12:1040–7.
Barciszewski J, Vrdmann VA. Noncoding RNAs: molecular biology and molecular medicine. Georgetown, TX/New York, NY. Landes Bioscience/Eurekah.com; Kluwer Academic/Plenum Publishers; 2003.
Brockdorff N, Ashworth A, Kay GF, Cooper P, Smith S, McCabe VM, et al. Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. Nature. 1991;351:329–31.
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