Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development

Abstract

Transcription factors are proteins that regulate gene expression by binding to cis-regulatory sequences such as promoters and enhancers. In embryonic stem (ES) cells, binding of the transcription factors OCT4, SOX2 and NANOG is essential to maintain the capacity of the cells to differentiate into any cell type of the developing embryo. It is known that transcription factors interact to regulate gene expression. In this study we show that combinatorial binding is strongly associated with co-localization of the transcriptional co-activator Mediator, H3K27ac and increased expression of nearby genes in embryonic stem cells. We observe that the same loci bound by Oct4, Nanog and Sox2 in ES cells frequently drive expression in early embryonic development. Comparison of mouse and human ES cells shows that less than 5% of individual binding events for OCT4, SOX2 and NANOG are shared between species. In contrast, about 15% of combinatorial binding events and even between 53% and 63% of combinatorial binding events at enhancers active in early development are conserved. Our analysis suggests that the combination of OCT4, SOX2 and NANOG binding is critical for transcription in ES cells and likely plays an important role for embryogenesis by binding at conserved early developmental enhancers. Our data suggests that the fast evolutionary rewiring of regulatory networks mainly affects individual binding events, whereas “gene regulatory hotspots” which are bound by multiple factors and active in multiple tissues throughout early development are under stronger evolutionary constraints.

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

“…Although this mechanism may maintain enhancers in a low-level open state, the absence of critical tissue-specific transcription factors could prevent downstream gene activation. Enhancers would become active and increase target gene expression only in tissues where the sufficient combination of transcription factors is available (Göke et al 2011).…”

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

“…Sox21 has not been previously studied in the early mouse embryo but is known to inhibit expression of the trophectoderm (TE) master gene Cdx2 in ES cells and is important for reprogramming (Kuzmichev et al, 2012). Furthermore, Sox21 expression is directly regulated by Sox2 (Chakravarthy et al, 2011;Kuzmichev et al, 2012;Mallanna et al, 2010), and its regulatory region is bound by Oct4 (Chakravarthy et al, 2011;Gö ke et al, 2011), which has heterogeneous nuclear-cytoplasmic kinetics at the 4-cell stage (Plachta et al, 2011). Together, this suggests that the heterogeneous Sox21 expression may itself be regulated by heterogeneous Oct4 and/or Sox2 activity in the embryo.…”

“…We focused on genes that are highly variable at the 4-cell stage and are targeted by Oct4 and/or Sox2 (including Sox21 [Chakravarthy et al, 2011;Gö ke et al, 2011]) and searched for subsets of genes whose expression patterns are coordinated. To this aim, the matrix of pairwise Spearman correlation coefficients was computed and hierarchical clustering was carried out (R function ''hclust,'' default options).…”

NANOG Plays a Hierarchical Role in the Transcription Network Regulating the Pluripotency and Plasticity of Adipose Tissue-Derived Stem Cells (ASCs)

“…These studies suggest that OCT4, SOX2, and NANOG can physically interact with each other and coordinately regulate target genes in some cases. Additionally, Goke and colleagues reported that combinatorial binding sites of the OCT4/SOX2/NANOG were more conserved between mouse and human ESCs than individual binding sites were [40,41].…”