Genome-wide analysis reveals a role for TDG in estrogen receptor-mediated enhancer RNA transcription and 3-dimensional reorganization

Bart Kolendowski,Joseph Torchia,Gobi Thillainadesan,Majdina Isovic,Alan B Tuck,Milica Krstic,Haider Hassan,Ann F Chambers

doi:10.1186/s13072-018-0176-2

Bart Kolendowski, Joseph Torchia + Show 6 more

Open Access

https://doi.org/10.1186/s13072-018-0176-2

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Abstract

BackgroundThe estrogen receptor (ER) is a ligand-dependant transcription factor expressed in many breast cancers and is the target of many endocrine-based cancer therapies. Genome-wide studies have shown that the ER binds to gene-specific enhancer regions in response to β-estradiol (E2) which undergo transcription producing noncoding enhancer RNA (eRNA). While eRNAs are important for transcriptional activation of neighboring genes, the mechanism remains poorly understood.ResultsUsing ChIP-Seq we generate a global profile of thymine DNA glycosylase (TDG), an ER coactivator that plays an essential role in DNA demethylation, in response to E2 in the MCF7 breast cancer cell line. Remarkably, we found that in response to E2 TDG localized to enhancers which also recruit ERα, RNA Pol II and other coregulators and which are marked by histone modifications indicative of active enhancers. Importantly, depletion of TDG inhibits E2-mediated transcription of eRNAs and transcription of ER-target genes. Functionally, we find that TDG both sensitizes MCF7 cells to tamoxifen-mediated cytostasis and increases migration and invasion of MCF7 cells.ConclusionsTaken together we find that TDG plays a central role in mediating transcription at a subset of enhancers and governs how MCF7 cells respond to both estrogenic and anti-estrogenic compounds and may be an effective therapeutic target.

Highlights

The estrogen receptor (ER) is a ligand-dependant transcription factor expressed in many breast cancers and is the target of many endocrine-based cancer therapies
To determine whether colocalization of thymine DNA glycosylase (TDG) and Estrogen receptor α (ERα) extends to other genomic locations, MCF7 cells were treated with 100 nM E2 for 45 min and ChIP-Seq was performed using a TDG-specific antibody
By retaining only peaks which appeared in both biological replicates we were able to identify 117 highly confident regions to which TDG localized in response to E2 (Additional File 3A and B)

Summary

Introduction

The estrogen receptor (ER) is a ligand-dependant transcription factor expressed in many breast cancers and is the target of many endocrine-based cancer therapies. Genome-wide studies have shown that the ER binds to gene-specific enhancer regions in response to β-estradiol (E2) which undergo transcription producing noncoding enhancer RNA (eRNA). While eRNAs are important for transcriptional activation of neighboring genes, the mechanism remains poorly understood. Steroid hormones such as 17β-estradiol (E2) coordinate complex gene programs and exert profound effects on cell growth, development and homeostasis [1]. Genome-wide studies using ChIP-based technologies have shown that the majority of ERα binding sites in breast cancer cells are found distally from gene promoters, and a significant component is found within genespecific “enhancer” regions in response to the E2 [2]. The exact mechanism governing eRNA transcription is unclear, recent evidence suggests that enhancer methylation status may play a role in eRNA production [6]

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