Integrative analysis of SF-1 transcription factor dosage impact on genome-wide binding and gene expression regulation

Mabrouka Doghman,Marco Volante,Enzo Lalli,Bonald C Figueiredo,Mauro Papotti

doi:10.1093/nar/gkt658

Abstract

Steroidogenic Factor-1 (SF-1) is a nuclear receptor that has a pivotal role in the development of adrenal glands and gonads and in the control of steroid hormone production, being also implicated in the pathogenesis of adrenocortical tumors. We have analyzed the mechanisms how SF-1 controls gene expression in adrenocortical cells and showed that it regulates different categories of genes according to its dosage. Significant correlations exist between the localization of SF-1-binding sites in chromatin under different dosage conditions and dosage-dependent regulation of gene expression. Our study revealed unexpected functional interactions between SF-1 and Neuron-Restrictive Silencer Factor/RE1-Silencing Transcription Factor (NRSF/REST), which was first characterized as a repressor of neuronal gene expression in non-neuronal tissues, in the regulation of gene expression in steroidogenic cells. When overexpressed, SF-1 reshapes the repertoire of NRSF/REST—regulated genes, relieving repression of key steroidogenic genes. These data show that NRSF/REST has a novel function in regulating gene expression in steroidogenic cells and suggest that it may have a broad role in regulating tissue-specific gene expression programs.

Highlights

Steroidogenic Factor-1 (SF-1/Ad4BP) is a transcription factor belonging to the nuclear receptor superfamily (NR5A1 in the nuclear receptor nomenclature) that was first identified as a regulator of the expression of steroidogenic P-450 enzymes in the adrenal cortex [1,2] and functions as a global regulator of steroidogenic gene expression [reviewed in [3]]
To identify the genes regulated by SF-1 in human adrenocortical cancer cells, we performed knockdown and overexpression experiments in the H295R/TR SF-1 cells, a subclone of the H295R cell line where SF-1 overexpression can be induced in a doxycycline-dependent manner [12]
Gene dosage is a critical determinant of their biological function, a paradigm case being represented by Oct-3/4 dosage in mouse embryonic stem cells [27]

Summary

Introduction

Steroidogenic Factor-1 (SF-1/Ad4BP) is a transcription factor belonging to the nuclear receptor superfamily (NR5A1 in the nuclear receptor nomenclature) that was first identified as a regulator of the expression of steroidogenic P-450 enzymes in the adrenal cortex [1,2] and functions as a global regulator of steroidogenic gene expression [reviewed in [3]]. SF-1 has a pivotal role in adrenogonadal development and differentiation into the steroidogenic lineage: mice lacking Sf1 have no adrenal glands and gonads, while its overexpression in the embryo induces formation of ectopic adrenal tissue [4,5,6]. Multiple factors regulate SF-1 activity: association with positive and negative cofactors, post-translational modifications, phospholipid ligand availability, epigenetic regulations and gene dosage [reviewed in [7]]. On the other side of the spectrum, SF-1 overexpression increases adrenocortical cancer cell proliferation and induces adrenocortical tumor formation in mice [12] and in humans is associated to adrenocortical tumorigenesis both in children [13] and adults [14]

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