In Vivo Genome-Wide PGR Binding in Pregnant Human Myometrium Identifies Potential Regulators of Labor

Abstract

The alterations in myometrial biology during labor are not well understood. The myometrium is the contractile portion of the uterus and contributes to labor, a process that may be regulated by the steroid hormone progesterone. Thus, human myometrial tissues from term pregnant in-active-labor (TIL) and term pregnant not-in-labor (TNIL) subjects were used for genome-wide analyses to elucidate potential future preventive or therapeutic targets involved in the regulation of labor. Using myometrial tissues directly subjected to RNA sequencing (RNA-seq), progesterone receptor (PGR) chromatin immunoprecipitation sequencing (ChIP-seq), and histone modification ChIP-seq, we profiled genome-wide changes associated with gene expression in myometrial smooth muscle tissue in vivo. In TIL myometrium, PGR predominantly occupied promoter regions, including the classical progesterone response element, whereas it bound mainly to intergenic regions in TNIL myometrial tissue. Differential binding analysis uncovered over 1700 differential PGR-bound sites between TIL and TNIL, with 1361 sites gained and 428 lost in labor. Functional analysis identified multiple pathways involved in cAMP-mediated signaling enriched in labor. A three-way integration of the data for ChIP-seq, RNA-seq, and active histone marks uncovered the following genes associated with PGR binding, transcriptional activation, and altered mRNA levels: ATP11A, CBX7, and TNS1. In vitro studies showed that ATP11A, CBX7, and TNS1 are progesterone responsive. We speculate that these genes may contribute to the contractile phenotype of the myometrium during various stages of labor. In conclusion, we provide novel labor-associated genome-wide events and PGR-target genes that can serve as targets for future mechanistic studies.

Assessment of the Epigenomic Landscape in Human Myometrium at Term Pregnancy

“…Variations could also arise from differences in the detection threshold. We identified an average of 44238 H3K27ac marked regions per specimen, while Dotts and colleagues found nearly 19000 per sample (Dotts, Reiman et al 2023). Reagent and sample handling could confound with biological variances of specimens leading to this difference.…”

JUND plays a genome-wide role in the quiescent to contractile switch in the pregnant human myometrium

“…Previous literature suggests a potential co-regulation of labor-driving genes, such as GJA1 , by AP-1 factors and PRs (Nadeem et al, 2016). To explore this association on a broader scale, we analyzed available ChIP-seq datasets of the PR cistrome and the histone mark H3K27ac, associated with active regulatory regions, from TNIL and TL human myometrium (Dotts et al ., 2022). These published datasets were compared with our JUND ChIP-seq datasets to identify overlapping peaks (Fig 3A).…”

“…Previous ChIP-seq experiments aimed at identifying PR-occupied regions in the myometrium revealed a significant enrichment of AP-1 motifs, suggesting an interaction between these factors in the myometrium (Wu et al, 2020; Dotts et al, 2022). Chromatin capture assays focusing on enhancers driving PR-regulated genes in the myometrium also indicated an overrepresentation of AP-1 motifs, reinforcing the genome-wide regulatory role of AP-1 in myometrial function (Wu et al, 2022).…”

“…Dysregulation in the signals that regulate the switch from the quiescent to contractile state can lead to premature labor or cause labour dystocia, resulting in the delivery of stillborn or underdeveloped infants at risk for complications later in life (Jehan et al ., 2009; Liu et al ., 2016; Chawanpaiboon et al ., 2019). Despite the plethora of gene expression data generated from the myometrium at varying states, including labor at term compared to non-laboring pregnant myometrium (Chan et al ., 2014; Stanfield et al ., 2019; Dotts et al ., 2022), non-pregnant versus term pregnant (Wu et al ., 2020), or depending upon the number of fetuses and timing of labor onset (Arrowsmith et al ., 2020), we currently lack an understanding of the molecular mechanisms that govern the regulation of these gene expression changes.…”

Integrative analysis of noncoding mutations identifies the druggable genome in preterm birth

“…To quantify the mutational consequence for each variant, we implemented our DEEP+ model to compute the absolute difference between the predicted chromatin openness scores from the genomic sequence centered on the two alleles of a given mutation. The same training procedure was used to construct the DEEP+ models on active enhancers or promoters marked by H3K27ac or H3K4me3, respectively, where the ChIP-seq data were obtained from GSE202027 ( 79 ).…”