Estrogen receptor α (ERα)-binding super-enhancers drive key mediators that control uterine estrogen responses in mice

Abstract

Estrogen receptor α (ERα) modulates gene expression by interacting with chromatin regions that are frequently distal from the promoters of estrogen-regulated genes. Active chromatin-enriched “super-enhancer” (SE) regions, mainly observed in in vitro culture systems, often control production of key cell type–determining transcription factors. Here, we defined super-enhancers that bind to ERα in vivo within hormone-responsive uterine tissue in mice. We found that SEs are already formed prior to estrogen exposure at the onset of puberty. The genes at SEs encoded critical developmental factors, including retinoic acid receptor α (RARA) and homeobox D (HOXD). Using high-throughput chromosome conformation capture (Hi-C) along with DNA sequence analysis, we demonstrate that most SEs are located at a chromatin loop end and that most uterine genes in loop ends associated with these SEs are regulated by estrogen. Although the SEs were formed before puberty, SE-associated genes acquired optimal ERα-dependent expression after reproductive maturity, indicating that pubertal processes that occur after SE assembly and ERα binding are needed for gene responses. Genes associated with these SEs affected key estrogen-mediated uterine functions, including transforming growth factor β (TGFβ) and LIF interleukin-6 family cytokine (LIF) signaling pathways. To the best of our knowledge, this is the first identification of SE interactions that underlie hormonal regulation of genes in uterine tissue and optimal development of estrogen responses in this tissue.

The estrogen receptor α cistrome in human endometrium and epithelial organoids

“…Enrichment of HOX motifs was previously noted in mouse uterine ESR1 peaks that lacked ERE motifs (58). An ESR1 binding super-enhancer was described at the mouse Hoxd cluster (52), and is present in the proliferative human endometrium (not shown). Mouse models with disruption of Hoxa 9,10,11 Hoxc 9 ,10,11 and Hoxd 9,10,11 exhibit impaired uterine development and function (59,60), and a mutation in HOXA11 was identified in a patient with a septate uterus (61).…”

Progesterone Signaling in Endometrial Epithelial Organoids

“…All new data are available on GEO (GSE200807). The following previously published sets were analyzed as part of the study: GSE132713 (endometrial PGR ChIPseq [ 18 ]), GSE69539 (hESC PGR ChIPseq [ 38 ]), mouse uterus GSE147843 (HiC [ 21 ]), GSE36455 (ESR1 and SMC1A ChIPseq [ 28 , 39 ]), GSE34927 (PGR ChIPseq [ 38 ])).…”

“…These TAD and loop structures bring distal enhancers into proximity with genes. HiC of mouse uterine chromatin [ 21 ] and of endometrial cancer cells [ 22 ] has been described. Chromatin conformation of normal human uterine epithelial cells has not been reported but would be valuable for finding ESR1 and PGR binding enhancer interactions with the target gene controlling epithelial receptivity.…”

Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response

“…The individual constituent enhancers within SEs can be functionally distinct, and constituent enhancers critical for SE function are referred to as hub enhancers (Huang et al, 2018). GR and estrogen receptor motifs are enriched in SEs in various cell lineages, including breast cancer cells (Bojcsuk et al, 2017;Shin et al, 2016), and SEs have been shown to control the estrogen response in the mouse uterus (Hewitt et al, 2020). Intriguingly, GR often binds to clusters of GBSs within and around target genes (Grange et al, 2001;Vockley et al, 2016;Chandler et al, 1983;Miranda et al, 2013).…”