Extensive Transcriptional Regulation of Chromatin Modifiers during Human Neurodevelopment

Abstract

Epigenetic changes, including histone modifications or chromatin remodeling are regulated by a large number of human genes. We developed a strategy to study the coordinate regulation of such genes, and to compare different cell populations or tissues. A set of 150 genes, comprising different classes of epigenetic modifiers was compiled. This new tool was used initially to characterize changes during the differentiation of human embryonic stem cells (hESC) to central nervous system neuroectoderm progenitors (NEP). qPCR analysis showed that more than 60% of the examined transcripts were regulated, and >10% of them had a >5-fold increased expression. For comparison, we differentiated hESC to neural crest progenitors (NCP), a distinct peripheral nervous system progenitor population. Some epigenetic modifiers were regulated into the same direction in NEP and NCP, but also distinct differences were observed. For instance, the remodeling ATPase SMARCA2 was up-regulated >30-fold in NCP, while it remained unchanged in NEP; up-regulation of the ATP-dependent chromatin remodeler CHD7 was increased in NEP, while it was down-regulated in NCP. To compare the neural precursor profiles with those of mature neurons, we analyzed the epigenetic modifiers in human cortical tissue. This resulted in the identification of 30 regulations shared between all cell types, such as the histone methyltransferase SETD7. We also identified new markers for post-mitotic neurons, like the arginine methyl transferase PRMT8 and the methyl transferase EZH1. Our findings suggest a hitherto unexpected extent of regulation, and a cell type-dependent specificity of epigenetic modifiers in neurodifferentiation.

Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach

“…H9 hESCs (as for UKK) were differentiated by dual SMAD inhibition as described earlier in detail (Balmer et al 2012; Chambers et al 2009; Weng et al 2012). Briefly, hESCs were plated as single cells at a density of 18,000 cells/cm² in medium previously conditioned for 24 h with mitomycin C-inactivated mouse embryonic fibroblasts, containing 10 μM ROCK inhibitor Y-27632 and 10 ng/ml bFGF.…”

“…To bridge this gap, embryonic stem cell (ESC)-based systems are currently being developed (Kuegler et al 2012; Leist et al 2008a; Weng et al 2012; Zimmer et al 2012). These systems recapitulate early neuronal development in vitro, including neurulation, patterning, neurogenesis and gliogenesis.…”

Histone Methylation in the Nervous System: Functions and Dysfunctions

“…Interestingly, a recent expression study comparing human cortical neurons to neural progenitor cells reports the transcriptional regulation of many chromatin modifiers during human neurodevelopment and identifies the arginine HMT PRMT8 and the lysine HMT EZH1 as new markers of postmitotic neurons [91].…”

Novel technologies and an overall strategy to allow hazard assessment and risk prediction of chemicals, cosmetics, and drugs with animal-free methods

“…the future will then bring higher throughput assays, better systems biology modeling, better integration of data from omics technologies, and better cell sources. For instance, we envisage that testing in non-transformed cell models, of murine (Sipes et al, 2011a) or preferentially of human origin, will require a further development of stem cell technology, to provide reliable cell sources (leist et al, 2008c;Zimmer et al, 2011aZimmer et al, ,b, 2012Weng et al, 2012;Balmer et al, 2012).…”