Pluripotency factors functionally premark cell-type-restricted enhancers in ES cells

Abstract

While enhancers for embryonic stem cell (ESC)-expressed genes and lineage-determining factors are characterized by conventional marks of enhancer activation in ESCs1,2,3, it remains unclear whether enhancers destined to regulate cell-type-restricted transcription units might also have some currently overlooked, distinct signatures in ESCs. Here, we report that cell-type-restricted enhancers, are unexpectedly premarked and activated as transcription units by the binding of a single, or two, ESC transcription factors, although not exhibiting traditional enhancer epigenetic marks in ESCs, thus uncovering the initial temporal origins of cell-type-restricted enhancers. This premarking is required for future cell-type-restricted enhancer activity in the differentiated cells, with the strength of the ESCs signature being functionally important for subsequent robustness of cell-type-restricted enhancer activation. This model has been experimentally validated in macrophage-restricted enhancers and neural precursor cells (NPCs)-restricted enhancers using ESCs-derived macrophages or NPCs, edited to contain specific ESC transcription factor motif deletions. The ESC transcription factor-determined DNA hydroxyl-methylation of the enhancers in ESCs may serve as a potential molecular memory for subsequent enhancer activation in the mature macrophage. These findings suggest that the massive repertoire of cell-type-restricted enhancers are essentially hierarchically and obligatorily “premarked” by binding of a defining ESC transcription factor in ESCs, dictating robustness of enhancer activation in mature cells.

Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification

“…Additionally, as in in vivo epiblast cells, we find that chromatin accessibility and DNA methylation profiles of ectoderm enhancers are also found to be accessible and unmethylated in mouse Embryonic Stem Cells (ESCs) ( Figure S27 ). This is consistent with a recent study describing enhancer priming for some lineage specific genes in ESCs 60 . Thus, ectoderm enhancers are epigenetically primed both in vivo and in vitro , while meso and endoderm enhancers only acquire their unique epigenetic state at the time of germ layer specification.…”

“…Hence, at least during gastrulation, lineages are defined by a hierarchical, or asymmetric, epigenetic model ( Figure 4c) .More generally, our discovery has important implications for the role of the epigenome in defining lineage commitment. Our work, and other recent studies also suggest chromatin priming may in certain circumstances precede overt cell fate decisions 26,60,66 . Additionally, we speculate that asymmetric epigenetic priming, where cells are epigenetically primed for a default cell type, may be a more general and poorly understood feature of differentiation and lineage commitment in vivo .…”

Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells

“…Similar results were obtained with data from hypomethylated naïve ESCs (Supplementary Figure 3C) (Kim et al 2018). Additionally, we found no evidence of other chromatin marks that could be maintaining TE enhancer activity repressed (Supplementary Figure 3D).…”

Transcription imparts architecture, function, and logic to enhancer units

“…Our dataset surveys a much larger number of clusters and indicates noncooperativity between adjacent elements, revealing a simple design for a max-activity filter of enhancer outputs. Indeed, a recent report of alternative TSS selection within distal enhancers during differentiation underscores broad implications of the max-activity filter 49 . This regulatory mechanism provides evolution a versatile tool for cellular decisions through winner-takes-all logic and may be easily adaptable for genetic engineering applications in agriculture and medicine.…”