title: In-silico identification and functional validation of allele-dependent AR enhancers.
abstract: Androgen Receptor (AR) and Estrogen Receptors (ERs) are key nuclear receptors that can cooperate in orchestrating gene expression programs in multiple tissues and diseases, targeting binding elements in promoters and distant enhancers. We report the unbiased identification of enhancer elements bound by AR and ER-α whose activity can be allele-specific depending on the status of nearby Single Nucleotide Polymorphisms (SNP). ENCODE data were computationally mined to nominate genomic loci with: (i) chromatin signature of enhancer activity from activation histone marks, (ii) binding evidence by AR and ER-α, (iii) presence of a SNP. Forty-one loci were identified and two, on 1q21.3 and 13q34, selected for characterization by gene reporter, Chromatin immunoprecipitation (ChIP) and RT-qPCR assays in breast (MCF7) and prostate (PC-3) cancer-derived cell lines. We observed allele-specific enhancer activity, responsiveness to ligand-bound AR, and potentially influence on the transcription of closely located genes (RAB20, ING1, ARHGEF7, ADAM15). The 1q21.3 variant, rs2242193, showed impact on AR binding in MCF7 cells that are heterozygous for the SNP. Our unbiased genome-wide search proved to be an efficient methodology to discover new functional polymorphic regulatory regions (PRR) potentially acting as risk modifiers in hormone-driven cancers and overall nominated SNPs in PRR across 136 transcription factors.
authors.affiliation: Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Sonia
authors.initials: S
authors.lastname: Garritano
authors.affiliation: Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Romanel
authors.affiliation: Laboratory of Transcriptional Networks, CIBIO, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Yari
authors.initials: Y
authors.lastname: Ciribilli
authors.affiliation: Laboratory of Transcriptional Networks, CIBIO, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Bisio
authors.affiliation: Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Antoneta
authors.initials: A
authors.lastname: Gavoci
authors.affiliation: Laboratory of Transcriptional Networks, CIBIO, Centre for Integrative Biology, University of Trento, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Inga
authors.affiliation: Laboratory of Computational Oncology, CIBIO, Centre for Integrative Biology, University of Trento, Italy.|HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, USA.|Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY, USA.
authors.forename: Francesca
authors.initials: F
authors.lastname: Demichelis
mesh_terms: D000483:Alleles; D015153:Blotting, Western; D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D047369:Chromatin Immunoprecipitation; D003198:Computer Simulation; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D047628:Estrogen Receptor alpha / Q000235:genetics* / Q000378:metabolism; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D011944:Receptors, Androgen / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014407:Tumor Cells, Cultured
chemical_list: C410798:AR protein, human; D047628:Estrogen Receptor alpha; D012333:RNA, Messenger; D011944:Receptors, Androgen
keywords: allele-specific; androgen receptor (AR); enhancer; estrogen receptor (ER); polymorphic regulatory regions