Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

Hawkins, R. David; Hon, Gary C.; Lee, Leonard K.; Ngo, Queminh; Lister, Ryan; Pelizzola, Mattia; Edsall, Lee; Kuan, Samantha; Luu, Ying; Klugman, Sarit; Antosiewicz‐Bourget, Jessica; Ye, Zhen; Espinoza, Celso A.; Agarwahl, Saurabh; Shen, Li; Ruotti, Victor; Wang, Wei; Stewart, Ron; Thomson, James A.; Ecker, Joseph R.; Ren, Bing

doi:10.1016/j.stem.2010.03.018

Cited by 756 publications

(794 citation statements)

References 73 publications

(85 reference statements)

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“…Nevertheless, these observations imply that A2UCOE simply supports the inherent epigenetic state and transcriptional activity of cellular promoters in P19 cells. This view is consistent with the fact that the MRP8 promoter in our vectors adopts the epigenetic state of its endogenous counterpart in ES cells (Supplementary Figure 3 and Harris et al 29 ; Hawkins et al 30 ; Wang et al 31 ). Accordingly, the A2UCOE chromatin remodeling activity does not interfere with the inherently encoded epigenetic state and transcriptional regulation of linked promoters, but prevents or reduces the influence of the chromosomal environment.…”

Section: Discussionsupporting

confidence: 89%

Physiological regulation of transgene expression by a lentiviral vector containing the A2UCOE linked to a myeloid promoter

et al. 2011

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Protection against epigenetic silencing is a desirable feature of future gene therapy vectors, in particular for those applications in which transgene expression will not confer growth advantage to gene-transduced cells. The ubiquitous chromatin opening element (UCOE) consisting of the methylation-free CpG island encompassing the dual divergently transcribed promoters of the human HNRPA2B1-CBX3 housekeeping genes (A2UCOE) has been shown to shield constitutive active heterologous promoters from epigenetic modifications and chromosomal position effects. However, it is unclear if this element can be used to improve expression from tissue-specific enhancer/promoters, while maintaining tissue specificity in hematopoietic cells. Here, we evaluated the potential of the A2UCOE in combination with the myeloid-specific myeloid related protein 8 (MRP8) promoter to target transgene expression specifically to myeloid cells in vitro and in vivo from a self-inactivating lentiviral vector. The inclusion of the A2UCOE did not interfere with specific upregulation of MRP8 promoter activity during myeloid differentiation and mediated sustained and vector copy-dependent expression in myeloid cells. Notably, the A2UCOE did not protect the MRP8 promoter from methylation in the P19 embryonal carcinoma cell line, suggesting that this element maintains the inherent epigenetic state and transcriptional activity of cellular promoters in their native configuration. Thus, the A2UCOE could represent a useful protective genetic element in gene therapy vectors, ensuring physiological transcriptional regulation of tissue-specific promoters independent of the chromosomal integration site.

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Section: Discussionsupporting

confidence: 89%

Physiological regulation of transgene expression by a lentiviral vector containing the A2UCOE linked to a myeloid promoter

et al. 2011

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“…Reprogramming of somatic cells into pluripotent stem cells requires changes in chromatin structure that mediate silencing of lineage-specific genes and activation of pluripotency genes [27,28]. Chromatin remodelers play active, regulatory roles during the reprogramming process, facilitating binding of transcription activators to regulatory gene sequences and upregulation of reprogramming factors [29].…”

Section: Discussionmentioning

confidence: 99%

NuRD Blocks Reprogramming of Mouse Somatic Cells into Pluripotent Stem Cells

et al. 2013

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Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) by overexpression of a defined set of transcription factors requires epigenetic changes in pluripotency genes. Nuclear reprogramming is an inefficient process and the molecular mechanisms that reset the epigenetic state during iPSC generation are largely unknown. Here, we show that downregulation of the nucleosome remodeling and deacetylation (NuRD) complex is required for efficient reprogramming. Overexpression of Mbd3, a subunit of NuRD, inhibits induction of iPSCs by establishing heterochromatic features and silencing embryonic stem cell-specific marker genes, including Oct4 and Nanog. Depletion of Mbd3, on the other hand, improves reprogramming efficiency and facilitates the formation of pluripotent stem cells that are capable of generating viable chimeric mice, even in the absence of c-Myc or Sox2. The results establish Mbd3/NuRD as an important epigenetic regulator that restricts the expression of key pluripotency genes, suggesting that drug-induced downregulation of Mbd3/ NuRD may be a powerful means to improve the efficiency and fidelity of reprogramming.

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“…Another comparative analysis was done on histone three lysine methylation by CHIP-Seq, with an improved computational method to detect not only peaks, but also long stretches of these marks [62]. This analysis highlighted the difference between human fibroblasts and pluripotent cells by showing that fibroblasts have more repressive chromatin due to the [24,27,28].…”

Section: Epigenetic Comparison Between Ipsc and Escmentioning

confidence: 99%