Genome-wide Estrogen Receptor-α activation is sustained, not cyclical.

Andrew N Holding,Amy E Cullen,Florian Markowetz

doi:10.7554/elife.40854

Andrew N Holding, Amy E Cullen + Show 1 more

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https://doi.org/10.7554/elife.40854

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Abstract

Estrogen Receptor-alpha (ER) drives 75% of breast cancers. Stimulation of the ER by estra-2-diol forms a transcriptionally-active chromatin-bound complex. Previous studies reported that ER binding follows a cyclical pattern. However, most studies have been limited to individual ER target genes and without replicates. Thus, the robustness and generality of ER cycling are not well understood. We present a comprehensive genome-wide analysis of the ER after activation, based on 6 replicates at 10 time-points, using our method for precise quantification of binding, Parallel-Factor ChIP-seq. In contrast to previous studies, we identified a sustained increase in affinity, alongside a class of estra-2-diol independent binding sites. Our results are corroborated by quantitative re-analysis of multiple independent studies. Our new model reconciles the conflicting studies into the ER at the TFF1 promoter and provides a detailed understanding in the context of the ER's role as both the driver and therapeutic target of breast cancer.

Highlights

The study of the Estrogen Receptor-a (ER) has played a fundamental role in both our understanding of transcription factors and cancer biology
To maximize the reproducibility of our results, MCF7 cells were grown from ATCC stocks, keeping passaging to a minimum, and the cell line origin was confirmed by STR genotyping
We found the sites at which we detected ER binding on the chromatin follows two distinct trajectories, either the rapid activation within 10 min followed by a stable response or ligand independent binding

Summary

Introduction

The study of the Estrogen Receptor-a (ER) has played a fundamental role in both our understanding of transcription factors and cancer biology. The ER is one of a family of transcription factors called nuclear receptors. Nuclear receptors are intra-cellular and, on activation by their ligand, typically undergo dimerisation and bind to specific DNA motif (for ER: Estrogen Response Elements; EREs). The nuclear receptor recruits a series of cofactors and promotes the basal transcription mechanism at either nearby promoters or through chromatin loops from distal enhancers. Because of the minimal nature of these systems relative to other signaling pathways, nuclear receptors have become a model system for transcription factor analysis. The role of nuclear receptors as drivers in a range of hormone dependent cancers has led to focused studies in the context of the disease

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