Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

Abstract

Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the regulatory mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole genome bisulfite sequencing, chromatin immunoprecipitation-sequencing and RNA-sequencing reveals unique events associated with specification towards each lineage. Dynamic alterations in DNA methylation and H3K4me1 are evident at putative distal regulatory elements bound by pluripotency factors or activated in specific lineages. In addition, we identified germ layer-specific H3K27me3 enrichment at sites exhibiting high DNA methylation in the undifferentiated state. A better understanding of these initial specification events will facilitate identification of deficiencies in current approaches leading to more faithful differentiation strategies as well as provide insights into the rewiring of human regulatory programs during cellular transitions.

Global delay in nascent strand DNA methylation

“…To compare methylation levels between gene bodies of expressed vs. non-expressed genes, bulk RNA-seq data was used from Gifford et al, Table S2 Ref 45 . Genes were binned into not expressed (FPKM < 1), expressed (FPKM > 10) and highly expressed (FPKM > 100).…”

Engineering of a Histone-Recognition Domain in Dnmt3a Alters the Epigenetic Landscape and Phenotypic Features of Mouse ESCs

“…WWD-Dnmt3a2 does not lower average gene expression levels in Group 1 ( Figure 3H) consistent with the safeguarding property of the ESC state against epigenetic transformation (Gifford et al, 2013;Xie et al, 2013). Alternatively, the relocation of WWDDnmt3a2 and the subsequent DNA hypermethylation might be insufficient to trigger transcriptional changes in actively expressed housekeeping genes.…”

Resetting the epigenome for heart regeneration.

“…There is a progressive compaction of nucleic material during differentiation of ESCs [58] and also during cardiomyocyte maturation [59]. Chromatin compaction and gene silencing are particularly prevalent at pluripotency loci and are coupled with a global shutdown of pluripotency in somatic cells [58]. This intimates a role of chromatin in not only controlling transcriptional output by TFs, but in a wider context, in controlling cellular differentiation and cell-lineage specification.…”

“…pluripotency > mesoderm > cardiac progenitors > cardiomyocytes) [56,57]. There is a progressive compaction of nucleic material during differentiation of ESCs [58] and also during cardiomyocyte maturation [59]. Chromatin compaction and gene silencing are particularly prevalent at pluripotency loci and are coupled with a global shutdown of pluripotency in somatic cells [58].…”