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Imprinted genes that regulate early mammalian growth are coexpressed in somatic stem cells.

Berg JS, Lin KK, Sonnet C, Boles NC, Weksberg DC, Nguyen H, Holt LJ, Rickwood D, Daly RJ, Goodell MA - PLoS ONE (2011)

Bottom Line: Here, we scrutinized data comparing genes expressed in murine long-term hematopoietic stem cells with their differentiated counterparts and observed that a disproportionate number were members of the developmentally-important, monoallelically expressed imprinted genes.Studying a subset, which are members of a purported imprinted gene network (IGN), we found their expression in HSCs rapidly altered upon hematopoietic perturbations.The parallel down-regulation of these genes postnatally in response to proliferation and differentiation suggests that the IGN could play a mechanistic role in both cell growth and tissue homeostasis.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

ABSTRACT
Lifelong, many somatic tissues are replenished by specialized adult stem cells. These stem cells are generally rare, infrequently dividing, occupy a unique niche, and can rapidly respond to injury to maintain a steady tissue size. Despite these commonalities, few shared regulatory mechanisms have been identified. Here, we scrutinized data comparing genes expressed in murine long-term hematopoietic stem cells with their differentiated counterparts and observed that a disproportionate number were members of the developmentally-important, monoallelically expressed imprinted genes. Studying a subset, which are members of a purported imprinted gene network (IGN), we found their expression in HSCs rapidly altered upon hematopoietic perturbations. These imprinted genes were also predominantly expressed in stem/progenitor cells of the adult epidermis and skeletal muscle in mice, relative to their differentiated counterparts. The parallel down-regulation of these genes postnatally in response to proliferation and differentiation suggests that the IGN could play a mechanistic role in both cell growth and tissue homeostasis.

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Real-time PCR analysis of imprinted gene expression in hematopoietic cells.Hematopoietic cell populations were isolated, and the expression of 10 core imprinted genes was determined by Q-RT-PCR. The data representing at least two independently isolated biological replicates for each population are shown as heat maps showing the fold difference in gene expression for each cell type compared to LT-HSCs. (A) Terminally differentiated cell populations (T-cells, B-cells, granulocytes, and erythrocytes) vs. HSCs. (B) Hematopoietic progenitor populations vs. LT-HSCs. (C) LT-HSC expression under conditions of acute (5-FU) or chronic (Lrg47−/−) proliferative stress vs. quiescence. Proliferating LT-HSCs were collected on day 6 post 5-FU treatment or from Lrg47−/− mice, and imprinted gene expression was determined by Q-RT-PCR.
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pone-0026410-g002: Real-time PCR analysis of imprinted gene expression in hematopoietic cells.Hematopoietic cell populations were isolated, and the expression of 10 core imprinted genes was determined by Q-RT-PCR. The data representing at least two independently isolated biological replicates for each population are shown as heat maps showing the fold difference in gene expression for each cell type compared to LT-HSCs. (A) Terminally differentiated cell populations (T-cells, B-cells, granulocytes, and erythrocytes) vs. HSCs. (B) Hematopoietic progenitor populations vs. LT-HSCs. (C) LT-HSC expression under conditions of acute (5-FU) or chronic (Lrg47−/−) proliferative stress vs. quiescence. Proliferating LT-HSCs were collected on day 6 post 5-FU treatment or from Lrg47−/− mice, and imprinted gene expression was determined by Q-RT-PCR.

Mentions: The imprinted genes exclusively or predominantly expressed in LT-HSCs bear a striking resemblance to a specific subset of imprinted genes referred to as the imprinted gene network (IGN) [16]. First identified through a meta-analysis of mouse gene-expression datasets, this group of genes is thought to be critically involved in the control of fetal and early postnatal growth, becoming down-regulated with the increasing age of the organism and slowing of the somatic growth rate [17]. Although others have reported subsets of this network (Table 1) [18], [19], [20], their link to a formal genetic program was often not recognized. Moreover, a number of the differentially expressed genes identified by our microarray analysis [11] are not part of the IGN as originally defined by Varrault et al [16]. Finally, we examined our previous microarray data for the 58 genes reported by Finkielstain et al. [21] to be down-regulated >3-fold between week-1 and week-4 of postnatal growth in heart, kidney and lung; 26 (44.8%) had flat expression profiles across hematopoietic populations, 13 genes (22.4%) were expressed in many or all lineages, and 10 genes (17.2%) were predominantly expressed in myeloid lineages. Quite strikingly, while the list of 58 genes reported by Finkielstain et al. contains 5 members of the IGN, it contains only 4 non-imprinted genes that are expressed predominantly in LT-HSCs (Sox4, Zfp184, Emelin1, and Smarca1). Thus, the genes that are down-regulated with age are not simply enriched for LT-HSC “fingerprint” genes, but are rather enriched for members of the IGN. These findings suggest that a specific group of imprinted genes, critical for embryonic growth but silenced in somatic tissues during early postnatal growth, remain expressed in LT-HSCs and may participate in the regulation of LT-HSC function. To explore this possibility, we selected 10 imprinted genes known to be coregulated during embryonic growth [16], [18], [19], [20], including three with indeterminate microarray expression (Cdkn1c, Igf2, and Mest) that were previously linked to hematopoiesis [22], [23], [24], [25]. Quantitative real-time PCR (Q-RT-PCR) was performed for these genes (Cdkn1c, Dlk1, Grb10, Gtl2, H19, Igf2, Mest, Ndn, Peg3, and Plagl1) in LT-HSCs and representative differentiated lineages, which had been purified independently of the original microarray study. This analysis showed that the coexpressed genes were at least 30-fold more abundant in LT-HSCs than in their differentiated progeny, with the exception of Igf2, Mest, and Plagl1, which retained some expression in T-cells (Figure 2A).


Imprinted genes that regulate early mammalian growth are coexpressed in somatic stem cells.

Berg JS, Lin KK, Sonnet C, Boles NC, Weksberg DC, Nguyen H, Holt LJ, Rickwood D, Daly RJ, Goodell MA - PLoS ONE (2011)

Real-time PCR analysis of imprinted gene expression in hematopoietic cells.Hematopoietic cell populations were isolated, and the expression of 10 core imprinted genes was determined by Q-RT-PCR. The data representing at least two independently isolated biological replicates for each population are shown as heat maps showing the fold difference in gene expression for each cell type compared to LT-HSCs. (A) Terminally differentiated cell populations (T-cells, B-cells, granulocytes, and erythrocytes) vs. HSCs. (B) Hematopoietic progenitor populations vs. LT-HSCs. (C) LT-HSC expression under conditions of acute (5-FU) or chronic (Lrg47−/−) proliferative stress vs. quiescence. Proliferating LT-HSCs were collected on day 6 post 5-FU treatment or from Lrg47−/− mice, and imprinted gene expression was determined by Q-RT-PCR.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3198398&req=5

pone-0026410-g002: Real-time PCR analysis of imprinted gene expression in hematopoietic cells.Hematopoietic cell populations were isolated, and the expression of 10 core imprinted genes was determined by Q-RT-PCR. The data representing at least two independently isolated biological replicates for each population are shown as heat maps showing the fold difference in gene expression for each cell type compared to LT-HSCs. (A) Terminally differentiated cell populations (T-cells, B-cells, granulocytes, and erythrocytes) vs. HSCs. (B) Hematopoietic progenitor populations vs. LT-HSCs. (C) LT-HSC expression under conditions of acute (5-FU) or chronic (Lrg47−/−) proliferative stress vs. quiescence. Proliferating LT-HSCs were collected on day 6 post 5-FU treatment or from Lrg47−/− mice, and imprinted gene expression was determined by Q-RT-PCR.
Mentions: The imprinted genes exclusively or predominantly expressed in LT-HSCs bear a striking resemblance to a specific subset of imprinted genes referred to as the imprinted gene network (IGN) [16]. First identified through a meta-analysis of mouse gene-expression datasets, this group of genes is thought to be critically involved in the control of fetal and early postnatal growth, becoming down-regulated with the increasing age of the organism and slowing of the somatic growth rate [17]. Although others have reported subsets of this network (Table 1) [18], [19], [20], their link to a formal genetic program was often not recognized. Moreover, a number of the differentially expressed genes identified by our microarray analysis [11] are not part of the IGN as originally defined by Varrault et al [16]. Finally, we examined our previous microarray data for the 58 genes reported by Finkielstain et al. [21] to be down-regulated >3-fold between week-1 and week-4 of postnatal growth in heart, kidney and lung; 26 (44.8%) had flat expression profiles across hematopoietic populations, 13 genes (22.4%) were expressed in many or all lineages, and 10 genes (17.2%) were predominantly expressed in myeloid lineages. Quite strikingly, while the list of 58 genes reported by Finkielstain et al. contains 5 members of the IGN, it contains only 4 non-imprinted genes that are expressed predominantly in LT-HSCs (Sox4, Zfp184, Emelin1, and Smarca1). Thus, the genes that are down-regulated with age are not simply enriched for LT-HSC “fingerprint” genes, but are rather enriched for members of the IGN. These findings suggest that a specific group of imprinted genes, critical for embryonic growth but silenced in somatic tissues during early postnatal growth, remain expressed in LT-HSCs and may participate in the regulation of LT-HSC function. To explore this possibility, we selected 10 imprinted genes known to be coregulated during embryonic growth [16], [18], [19], [20], including three with indeterminate microarray expression (Cdkn1c, Igf2, and Mest) that were previously linked to hematopoiesis [22], [23], [24], [25]. Quantitative real-time PCR (Q-RT-PCR) was performed for these genes (Cdkn1c, Dlk1, Grb10, Gtl2, H19, Igf2, Mest, Ndn, Peg3, and Plagl1) in LT-HSCs and representative differentiated lineages, which had been purified independently of the original microarray study. This analysis showed that the coexpressed genes were at least 30-fold more abundant in LT-HSCs than in their differentiated progeny, with the exception of Igf2, Mest, and Plagl1, which retained some expression in T-cells (Figure 2A).

Bottom Line: Here, we scrutinized data comparing genes expressed in murine long-term hematopoietic stem cells with their differentiated counterparts and observed that a disproportionate number were members of the developmentally-important, monoallelically expressed imprinted genes.Studying a subset, which are members of a purported imprinted gene network (IGN), we found their expression in HSCs rapidly altered upon hematopoietic perturbations.The parallel down-regulation of these genes postnatally in response to proliferation and differentiation suggests that the IGN could play a mechanistic role in both cell growth and tissue homeostasis.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

ABSTRACT
Lifelong, many somatic tissues are replenished by specialized adult stem cells. These stem cells are generally rare, infrequently dividing, occupy a unique niche, and can rapidly respond to injury to maintain a steady tissue size. Despite these commonalities, few shared regulatory mechanisms have been identified. Here, we scrutinized data comparing genes expressed in murine long-term hematopoietic stem cells with their differentiated counterparts and observed that a disproportionate number were members of the developmentally-important, monoallelically expressed imprinted genes. Studying a subset, which are members of a purported imprinted gene network (IGN), we found their expression in HSCs rapidly altered upon hematopoietic perturbations. These imprinted genes were also predominantly expressed in stem/progenitor cells of the adult epidermis and skeletal muscle in mice, relative to their differentiated counterparts. The parallel down-regulation of these genes postnatally in response to proliferation and differentiation suggests that the IGN could play a mechanistic role in both cell growth and tissue homeostasis.

Show MeSH
Related in: MedlinePlus