Estrogen represses gene expression through reconfiguring chromatin structures

Abstract

Estrogen regulates over a thousand genes, with an equal number of them being induced or repressed. The distinct mechanisms underlying these dual transcriptional effects remain largely unknown. We derived comprehensive views of the transcription machineries assembled at estrogen-responsive genes through integrating multiple types of genomic data. In the absence of estrogen, the majority of genes formed higher-order chromatin structures, including DNA loops tethered to protein complexes involving RNA polymerase II (Pol II), estrogen receptor alpha (ERα) and ERα-pioneer factors. Genes to be 'repressed' by estrogen showed active transcription at promoters and throughout the gene bodies; genes to be 'induced' exhibited active transcription initiation at promoters, but with transcription paused in gene bodies. In the presence of estrogen, the majority of estrogen-induced genes retained the original higher-order chromatin structures, whereas most estrogen-repressed genes underwent a chromatin reconfiguration. For estrogen-induced genes, estrogen enhances transcription elongation, potentially through recruitment of co-activators or release of co-repressors with unique roles in elongation. For estrogen-repressed genes, estrogen treatment leads to chromatin structure reconfiguration, thereby disrupting the originally transcription-efficient chromatin structures. Our in silico studies have shown that estrogen regulates gene expression, at least in part, through modifying previously assembled higher-order complexes, rather than by facilitating de novo assembly of machineries.

Figure 1.

Transcription states and chromatin complexes in the absence of estrogen. (A) Composite (meta-gene) profiles of Pol II ChIP-seq of estrogen-responsive genes, presented as RPM. Profiles for promoter and 3′ end were aligned at TSS and TES respectively; profiles for gene bodies were scaled. (B) Annotation of genes based on their relative position to the Pol chromatin complex. (C) Distribution of estrogen-responsive genes in terms of their relative position to Pol II complexes. (D) Meta-gene profiles of GRO-seq of Pol II bound anchor genes, presented as RPM. Profiles for promoter and 3′ end were aligned at TSS and TES, respectively; profiles for gene bodies were scaled. GRO-seq reads aligned to RefSeq TSSs in both sense and antisense directions relative to the direction of the gene. (E) Boxplots show the comparison of pause ratio (TSS/gene body) for estrogen-repressed genes (blue) and estrogen-induced genes (coral) as determined by GRO-seq in the absence ligand.

Figure 2.

Comparison of transcription states of the estrogen-induced and estrogen-repressed genes. (A) Comparison of meta-gene profiles of Pol II ChIP-seq of estrogen-induced and estrogen-repressed genes in the absence (blue) and in the presence of estrogen (pink), presented as RPM. (B) Comparison of de novo transcription of estrogen-induced and estrogen-repressed genes in the absence (blue) and in the presence of estrogen (pink) determined by GRO-seq for the estrogen-induced (left) and estrogen-repressed (right) genes.

Figure 3.

A Venn diagram illustrating the overlap between the Pol II complexes formed in the absence of ligand and the ERα complexes formed in the presence of ligand.

Figure 4.

The position transition patterns of estrogen-responsive genes with respect to Pol II and ERα complexes and examples of positional transition of genes with respect to Pol II and ERα ChIA-PET complexes. (A) anchor-to-anchor, (B) anchor-to-loop, (C) anchor-to-stand-alone. A brown arrow represents a gene. The figure shows the positions and relationships of genes (RefSeq), Pol II complex anchor regions (Pol II Int), ERα complex anchor regions (ERα Int) and ERα ChIP-seq binding sites in the absence and presence of estrogen for three example genes: (A) anchor-to-anchor, gene: MYB; (B) anchor-to-loop, gene: CALM1; (C) anchor-to-stand-alone, gene: TLE1. The estrogen treatment conditions are color-coded with green (absence) and red (presence). The black arrows indicate one of Pol II anchor regions in the absence of ligand; a line in the chromatin interaction graph indicate the DNA region is involved in a chromatin complex.

Figure 5.

The distribution of the positional transitions of the estrogen-induced and estrogen-repressed genes. This figure shows the impact of estrogen treatment on chromatin reconfiguration (a gene within a Pol II anchor region was categorized as a loop or standalone gene with respect to ER complex after estrogen treatment) (A) Number of gene in each positional transitional pattern group (anchor-to-anchor, anchor-to-loop, anchor-to-stand-alone) for estrogen-induced and estrogen-repressed genes. (B) Positional transition pattern distribution of estrogen-responsive genes that had ERα binding in the anchor region of the original Pol II complexes in the absence of ligand.

Figure 6.

An example of integrative view of the transcription machinery at a gene. The figure shows the Pol II and ERα ChIA-PET data and ChIP-seq data in the vicinity of MYB gene in the absence (−) and presence (+) of estrogen. For the chromatin-interaction trace, a line indicates the DNA region is part of a chromatin structure, and a bar shows one of the anchor regions, where DNA interacts with a protein complex. For ChIP-seq data, a block indicates a DNA–protein binding site.