Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis

Attema, Joanne L.; Papathanasiou, Peter; Forsberg, Erik; Xu, Jian; Smale, Stephen T.

doi:10.1073/pnas.0704468104

Cited by 133 publications

(137 citation statements)

References 51 publications

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“…Our observations reinforce the idea that the presence of bivalent me 3 K4/me 3 K27 H3 is not ES cell or stem cell specific. As such, the modification may act to maintain loci in a dormant state with the potential for activation and this may occur in a array of cell types (15,17,20,(32)(33)(34)(35)(36).…”

Section: Resultsmentioning

confidence: 99%

A histone demethylase is necessary for regeneration in zebrafish

Stewart

Tsun

Belmonte

2009

Proc. Natl. Acad. Sci. U.S.A.

106

107

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Urodele amphibians and teleost fish regenerate amputated body parts via a process called epimorphic regeneration. A hallmark of this phenomenon is the reactivation of silenced developmental regulatory genes that previously functioned during embryonic patterning. We demonstrate that histone modifications silence promoters of numerous genes involved in zebrafish caudal fin regeneration. Silenced developmental regulatory genes contain bivalent me 3 K4/me 3 K27 H3 histone modifications created by the concerted action of Polycomb (PcG) and Trithorax histone methyltransferases. During regeneration, this silent, bivalent chromatin is converted to an active state by loss of repressive me 3 K27 H3 modifications, occurring at numerous genes that appear to function during regeneration. Loss-of-function studies demonstrate a requirement for a me 3 K27 H3 demethylase during fin regeneration. These results indicate that histone modifications at discreet genomic positions may serve as a crucial regulatory event in the initiation of fin regeneration.chromatin ͉ polycomb

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Section: Resultsmentioning

confidence: 99%

A histone demethylase is necessary for regeneration in zebrafish

Stewart

Tsun

Belmonte

2009

Proc. Natl. Acad. Sci. U.S.A.

106

107

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“…Epigenetic silencing of lineage-inappropriate genes takes place progressively and chromatin becomes less and less plastic during hematopoietic differentiation (Tagoh et al, 2004;Attema et al, 2007;Walter et al, 2008). For that reason, ectopic activation of CD19 and PAX5 most likely occurs at an early stage of hematopoietic differentiation.…”

Section: Discussionmentioning

confidence: 99%

Aberrant expression of CD19 in AML with t(8;21) involves a poised chromatin structure and PAX5

et al. 2010

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Correct hematopoietic differentiation requires the tightly regulated execution of lineage-specific and stage-restricted gene expression programs. This process is disturbed in hematological malignancies that typically show incomplete differentiation but often also display a mixed lineage phenotype. Co-expression of lymphoid and myeloid molecules is a well-known feature of acute myeloblastic leukemia (AML) with t(8;21). These cells consistently express the B-cell-specific transcription factor PAX5, and the B-cell-specific cell surface protein CD19. However, the functional consequences of PAX5 expression are unknown. To address this question, we studied the chromatin features of CD19, which is a direct target of PAX5 in cells with and without the t(8;21) chromosomal translocation. We show that CD19 chromatin exists in a poised configuration in myeloid progenitors and that this poised chromatin structure facilitates PAX5-dependent CD19 activation. Our results also show a positive correlation between PAX5 and CD19 expression in t(8;21)-positive AML cells and demonstrate that PAX5 binds to the promoter and enhancer of CD19 gene and remodels chromatin structure at the promoter. This study shows that expression of PAX5 in leukemic cells has functional consequences and points to an important role of a progenitor-specific chromatin configuration in myeloid leukemia.

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“…ChIP on isolated CSM4B cells was performed as described in Attema et al (2007). The immunoprecipitated DNA was recovered using a PCR purification kit (QIAGEN) and was used as template in PCR with specific primers spanning the HD and PD binding site of Id3 promoter.…”

Section: Chromatin Immunoprecipitation (Chip) Assaymentioning

confidence: 99%

Id3 Is a Direct Transcriptional Target of Pax7 in Quiescent Satellite Cells

Kumar

Shadrach

Wagers

et al. 2009

MBoC

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INTRODUCTIONPax3 and Pax7 are two closely related transcription factors that are expressed in the dermomyotome, and they have been shown to be essential for generation of all fetal trunk musculature . Pax3/7-expressing dermomyotomal cells have recently been shown to give rise to skeletal muscle progenitors, termed satellite cells, in the adult (Gros et al., 2005;Kassar-Duchossoy et al., 2005;Relaix et al., 2005;Schienda et al., 2006). Satellite cells are a small population of myogenic progenitors that reside between the sarcolemma and basal lamina of the muscle fiber, and they play a crucial role in postnatal muscle growth and regeneration (reviewed in Zammit et al., 2006). Following skeletal muscle injury or exercise-induced activation, the normally quiescent Pax7-expressing satellite cells proliferate extensively and up-regulate expression of MyoD (Smith et al., 2001;Yan et al., 2003;Montarras et al., 2005) and Myf-5 (Conboy and Rando, 2002;Yan et al., 2003), before differentiation into skeletal muscle.Pax3 and Pax7 are members of the Pax transcription factor family and contain both paired (PD) and homeodomain (HD) DNA binding motifs. Pax3 and Pax7 can bind to DNA sequences containing either a consensus paired domain binding site (GTCAC A/G C/G A/T T/C) or a homeodomain binding site (ATTA) (Chalepakis et al., 1994;Chalepakis and Gruss, 1995). Pax3 and Pax7 activate MyoD expression (Maroto et al., 1997;Tajbakhsh et al., 1997;Relaix et al., 2003Relaix et al., , 2004, and recently Pax3 has been shown to directly bind sequences that regulate the expression of either MyoD in C2C12 cells (Hu et al., 2008) or Myf-5 during development of hypaxial muscle (Bajard et al., 2006). Although it is clear that Pax3/7 can directly induce the expression of Myf5 (Bajard et al., 2006), MyoD (Hu et al., 2008), and fibroblast growth factor receptor 4 (Lagha et al., 2008), other relevant targets for Pax3/7 in satellite cells have yet to be identified. To identify potential targets for Pax3/7 in satellite cells, we examined the transcriptional profile of genes induced by these transcription factors in the C2C12 muscle cell line. Of the genes identified, we found that a subset were also expressed in quiescent satellite cells and therefore they could potentially be direct targets of Pax7 in these cells. In this report, we focus on two such putative Pax3/7 transcriptional targets, inhibitor of DNA binding (Id) 2 and Id3, which we found to be expressed in quiescent satellite cells. We report that Pax3/7 can drive expression of both Id2 and Id3 in C2C12 cells under low serum conditions, that the Id3 promoter contains a conserved Pax3/7 binding site, and that Pax3/7 can activate expression of a reporter construct driven by the Id3 promoter. In addition, we demonstrate that Pax7 is normally bound to the Id3 promoter in quiescent satellite cells and that short hairpin RNA (shRNA)-mediated knockdown of Pax7 expression in cultured satellite cells Abbreviations used: C1R, complement component 1 R subunit; ChIP, chromatin immunoprecipitation; CS...

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Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis

Cited by 133 publications

References 51 publications

A histone demethylase is necessary for regeneration in zebrafish

A histone demethylase is necessary for regeneration in zebrafish

Aberrant expression of CD19 in AML with t(8;21) involves a poised chromatin structure and PAX5

Id3 Is a Direct Transcriptional Target of Pax7 in Quiescent Satellite Cells

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