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Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'

Abstract

We combined large-scale mRNA expression analysis and gene mapping to identify genes and loci that control hematopoietic stem cell (HSC) function. We measured mRNA expression levels in purified HSCs isolated from a panel of densely genotyped recombinant inbred mouse strains. We mapped quantitative trait loci (QTLs) associated with variation in expression of thousands of transcripts. By comparing the physical transcript position with the location of the controlling QTL, we identified polymorphic cis-acting stem cell genes. We also identified multiple trans-acting control loci that modify expression of large numbers of genes. These groups of coregulated transcripts identify pathways that specify variation in stem cells. We illustrate this concept with the identification of candidate genes involved with HSC turnover. We compared expression QTLs in HSCs and brain from the same mice and identified both shared and tissue-specific QTLs. Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of coregulated transcripts.

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Figure 1: Mapping QTLs that modulate gene expression in HSCs.
Figure 2: Comparison of brain and HSC QTLs.
Figure 3: Linkage analysis of four strongly cis-regulated stem cell transcripts showing genome-wide significant linkage to an interval mapping in close proximity to the gene (gene position is indicated by red triangle).
Figure 4: Candidate genes affecting HSC proliferation.

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Acknowledgements

We thank G. Mesander and H. Moes for flow cytometry support and O. Sibon and R. van Os for critically reading the manuscript. This work was supported by grants from the Royal Netherlands Academy of Sciences, a Genomics Fellowship from the Netherlands Organization for Scientific Research, the Dutch Cancer Society and the National Heart, Lung, and Blood Institute (to G.d.H.) and by the National Institute of Mental Health, National Institute on Drug Abuse, the National Institute on Alcohol Abuse and Alcoholism and the National Science Foundation (to R.W.W.).

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Correspondence to Gerald de Haan.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Stem cell frequency in BXd mice. (XLS 28 kb)

Supplementary Table 2

Cis-regulated stem cell transcripts. (XLS 43 kb)

Supplementary Table 3

Trans-regulated stem cell transcripts. (XLS 43 kb)

Supplementary Table 4

Stable cis-regulated transcripts. (XLS 29 kb)

Supplementary Table 5

Stable trans-regulated transcripts. (XLS 70 kb)

Supplementary Table 6

Polymorphisms in the Scp2 candidate genes. (XLS 27 kb)

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Bystrykh, L., Weersing, E., Dontje, B. et al. Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat Genet 37, 225–232 (2005). https://doi.org/10.1038/ng1497

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