The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo

Abstract

Poised enhancers (PEs) represent a genetically distinct set of distal regulatory elements that control the expression of major developmental genes. Before becoming activated in differentiating cells, PEs are already bookmarked in pluripotent cells with unique chromatin and topological features that could contribute to their privileged regulatory properties. However, since PEs were originally characterized in embryonic stem cells (ESC), it is currently unknown whether PEs are functionally conserved in vivo. Here, we show that the chromatin and 3D structural features of PEs are conserved among mouse pluripotent cells both in vitro and in vivo. We also uncovered that the interactions between PEs and their target genes are globally controlled by the combined action of Polycomb, Trithorax and architectural proteins. Moreover, distal regulatory sequences located close to developmental genes and displaying the typical genetic (i.e. CpG islands) and chromatin (i.e. high accessibility and H3K27me3 levels) features of PEs are commonly found across vertebrates. These putative PEs show high sequence conservation within specific vertebrate clades, with only a few being evolutionary conserved across all vertebrates. Lastly, by genetically disrupting PEs in mouse and chicken embryos, we demonstrate that these regulatory elements play essential roles during the induction of major developmental genes in vivo.

Transcriptional enhancers and their communication with gene promoters

“…Finally, some enhancers are marked with H3K27me3 alone and are considered to be “Polycomb-repressed” [ 139 – 141 ]. Many developmental enhancers are found in the poised or Polycomb-repressed state in early development [ 139 , 142 , 143 ], and the functional role of these states remains an area of active research. One possibility is that poised enhancers may be ‘held in check’ for rapid activation [ 144 ].…”

SOX15 regulates stem cell pluripotency and promotes neural fate during differentiation by activating Hes5

“…Because SOX2 recruitment to the Hes5 locus does not appear to be affected by the absence of SOX15 in KO ESCs, we propose that transcriptional activation of Hes5 by SOX15 likely requires other TFs and coactivators that are induced at the onset of neural differentiation, in conjunction with epigenetic remodeling at the Hes5 gene locus (108). The pre-binding of SOX15 at the Hes5 locus may represent a common strategy by which developmentally poised genes are regulated upon differentiation (109).…”

Polycomb Repressive Complex 2 in Eukaryotes—An Evolutionary Perspective

“…In mammals, H3K27me3 has two distribution patterns: large domains (>100 kb) encompassing the Hox loci and smaller domains of a few kilobases (reviewed by the authors of [ 75 ]). In addition to genic loci, H3K27me3 and PRC2 reside in poised enhancers (PEs) that often associate with bivalent genes in vertebrate pluripotent cells [ 152 ]. While PRC1 contributes to the PE marking globally [ 152 ] and also targets active enhancers in cancer cells [ 153 ], PRC2 is involved at PEs at specific loci [ 152 ].…”

“…In addition to genic loci, H3K27me3 and PRC2 reside in poised enhancers (PEs) that often associate with bivalent genes in vertebrate pluripotent cells [ 152 ]. While PRC1 contributes to the PE marking globally [ 152 ] and also targets active enhancers in cancer cells [ 153 ], PRC2 is involved at PEs at specific loci [ 152 ]. Unlike in animals, the distribution of H3K27me3 in A. thaliana is usually limited to single genes, with the modification covering proximal parts of promoters and gene bodies with average enrichment regions of 1–1.5 kb [ 37 , 38 , 154 , 155 ].…”