Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers.

Fabienne Bejjani,Laurent Vallar,Claire Tolza,Charles-Henri Lecellier,Isabelle Jariel-Encontre,Laurent Brehelin,Hughes Parrinello,Damien Downes,Tony Kaoma,Muhammad Ahmad Maqbool,Jim R Hughes,Mathias Boulanger,Jean-Christophe Andrau,Amal Zine El Aabidine,Marine Rohmer,Marc Piechaczyk,Sophie Lebre,Kazem Zibara,Raphaël Romero

doi:10.1093/nar/gkab053

Abstract

The ubiquitous family of dimeric transcription factors AP-1 is made up of Fos and Jun family proteins. It has long been thought to operate principally at gene promoters and how it controls transcription is still ill-understood. The Fos family protein Fra-1 is overexpressed in triple negative breast cancers (TNBCs) where it contributes to tumor aggressiveness. To address its transcriptional actions in TNBCs, we combined transcriptomics, ChIP-seqs, machine learning and NG Capture-C. Additionally, we studied its Fos family kin Fra-2 also expressed in TNBCs, albeit much less. Consistently with their pleiotropic effects, Fra-1 and Fra-2 up- and downregulate individually, together or redundantly many genes associated with a wide range of biological processes. Target gene regulation is principally due to binding of Fra-1 and Fra-2 at regulatory elements located distantly from cognate promoters where Fra-1 modulates the recruitment of the transcriptional co-regulator p300/CBP and where differences in AP-1 variant motif recognition can underlie preferential Fra-1- or Fra-2 bindings. Our work also shows no major role for Fra-1 in chromatin architecture control at target gene loci, but suggests collaboration between Fra-1-bound and -unbound enhancers within chromatin hubs sometimes including promoters for other Fra-1-regulated genes. Our work impacts our view of AP-1.

Highlights

AP-1 is a ubiquitous family of dimeric transcription factors (TF) that was identified >30 years ago
The anti-p300/CBP antibody Ab14984 was used in Chromatin immunoprecipitations (ChIPs)-seq experiments conducted on MDA-MB-231 cells grown under standard cell culture conditions (Figure 5A), as well as in ChIP-qPCR experiments carried out on MDAMB-231 cells transfected with either a control siRNA or siRNAs directed against Fra-1 or Fra-2 (Figure 5C, right panels)
Human MDA-MB-231 cells have been employed in this study, as they constitute the most widely used and documented reference triple negative breast cancers (TNBCs) cell line model

Summary

Introduction

AP-1 is a ubiquitous family of dimeric transcription factors (TF) that was identified >30 years ago (reviewed in [1]). AP1 includes the members of the ATF (ATF-2, ATF3/LRF1, ATF-4, ATF-5, ATF-6B, ATF-7, BATF, BATF2, BATF-3, JDP2) and MAF (c-MAF, MAFA, -B, -F, -G, -K and Nrl) multigene families (see [1]) The expression of the latter proteins is more tissue/cell-specific than that of Fos and Jun proteins [2]. Central in the biology of all of these proteins is the so-called bZIP domain made up of a basic domain allowing recognition of specific DNA motifs and an adjacent leucine zipper domain responsible for protein homo/heterodimerization. Depending on their composition, AP-1 dimers bind to specific types of palindromic sequences and their variants. Fos:Jun and Jun:Jun dimers preferentially bind DNA motifs referred to as 12-O-tetradecanoylphorbol-13-acetate (TPA)responsive element (TRE; called AP-1 motif), ATFcontaining dimers preferentially bind to cAMP-responsive element (CRE) whereas MAF-containing dimers bind either MARE I or MARE II motifs that are extensions of TRE and CRE motifs, respectively [2]

Methods

Results

Conclusion