Abstract
Epigenetic modifications play a crucial role in neurogenesis, learning, and memory, but the study of their role in early neuroectoderm commitment from pluripotent inner cell mass is relatively lacking. Here we utilized the system of directed neuroectoderm differentiation from human embryonic stem cells and identified that KDM6B, an enzyme responsible to erase H3K27me3, was the most upregulated enzyme of histone methylation during neuroectoderm differentiation by transcriptome analysis. We then constructed KDM6B-null embryonic stem cells and found strikingly that the pluripotent stem cells with KDM6B knockout exhibited much higher neuroectoderm induction efficiency. Furthermore, we constructed a series of embryonic stem cell lines knocking out the other H3K27 demethylase KDM6A, and depleting both KDM6A and KDM6B, respectively. These cell lines together confirmed that KDM6 impeded early neuroectoderm commitment. By RNA-seq, we found that the expression levels of a panel of WNT genes were significantly affected upon depletion of KDM6. Importantly, the result that WNT agonist and antagonist could abolish the differential neuroectoderm induction due to manipulating KDM6 further demonstrated that WNT was the major downstream of KDM6 during early neural induction. Moreover, we found that the chemical GSK-J1, an inhibitor of KDM6, could enhance neuroectoderm induction from both embryonic stem cells and induced pluripotent stem cells. Taken together, our findings not only illustrated the important role of the histone methylation modifier KDM6 in early neurogenesis, providing insights into the precise epigenetic regulation in cell fate determination, but also showed that the inhibitor of KDM6 could facilitate neuroectoderm differentiation from human pluripotent stem cells.
Highlights
Cell fate determination involves a series of precise regulation of temporal and spatial gene expression
We checked some publicly available expression data set on neuroectoderm differentiation, and the result from LIBD Stem Cell Browser based on multiple differentiation conditions and cell lines3 consistently supported that KDM6B was significantly upregulated during neural progenitor differentiation (Supplementary Figure 1)
We identified the role of KDM6A and KDM6B in human neuroectoderm commitment
Summary
Cell fate determination involves a series of precise regulation of temporal and spatial gene expression. Epigenetic changes, including histone modification, DNA methylation, and chromatin remodeling, are critically required for the generation of cell diversity during development (Podobinska et al, 2017). Among the histone tail modifications, trimethylation of lysine 27 on KDM6 and Human Neuroectoderm Differentiation histone 3 (H3K27me3) and trimethylation of lysine 4 on histone 3 (H3K4me3), which play an important role in gene repression and activation, respectively, are reported to be deposited in the promoters of developmental genes in embryonic stem cells (ESCs), well known as the bivalent state (Bernstein et al, 2006). KDM6 family members include catalytically active KDM6A ( UTX) and KDM6B ( JMJD3) sharing a well-conserved JmjC histone demethylation domain, while KDM6C ( UTY) is considered with no catalytic activity (Sengoku and Yokoyama, 2011; Jones et al, 2018; Gazova et al, 2019). Mouse with Kdm6a knockout exhibits slightly different phenotype between male and female: the female Kdm6a-knockout mouse shows higher mortality rate and exhibited anxiety-like behaviors than male (Shpargel et al, 2012; Tang et al, 2017)
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