title: Functional genomic methods to study estrogen receptor activity.
abstract: Estrogen Receptor (ER) is a nuclear receptor that mediates the actions of estrogen and tamoxifen. ER is expressed in a major fraction of human breast cancers. Recently, genomic maps for estrogen- and tamoxifen-ER have been published. Interestingly, estrogen and tamoxifen induce similar genomic interactions and both ligands have been shown to use co-operating factors. The interactions of these co-operating factors within ER regions have impact both on ER-DNA interactions and gene expression regulated by estrogen and tamoxifen. Moreover, the study of chromatin changes induced by these factors has also provided significant insight into our understanding of ER transcriptional regulation. This methods review describes some functional genomic methods to study the influence of both ER ligands and ER co-operating factors. The analysis of protein-DNA interactions and chromatin changes can be explored by using classical and novel methods such as Chromatin Immunoprecipitation (ChIP) or Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE). This review also explores the properties of each of these methods and the advantages of combining them with high throughput sequencing.
authors.affiliation: Breast Cancer Research group, Nordic EMBL Partnership, Centre for Molecular Medicine Norway, University of Oslo, Blindern, Oslo, Norway.
authors.forename: Siv
authors.initials: S
authors.lastname: Gilfillan
authors.forename: Elisa
authors.initials: E
authors.lastname: Fiorito
authors.forename: Antoni
authors.initials: A
authors.lastname: Hurtado
mesh_terms: D000818:Animals; D018931:Antineoplastic Agents, Hormonal / Q000378:metabolism / Q000494:pharmacology; D001943:Breast Neoplasms / Q000188:drug therapy / Q000378:metabolism*; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D003432:Cross-Linking Reagents / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D004967:Estrogens / Q000378:metabolism; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D023281:Genomics / Q000379:methods*; D006801:Humans; D008024:Ligands; D042361:Mammary Glands, Human / Q000187:drug effects / Q000378:metabolism*; D009363:Neoplasm Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011960:Receptors, Estrogen / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D050436:Regulatory Elements, Transcriptional / Q000187:drug effects; D020218:Response Elements / Q000187:drug effects; D020845:Selective Estrogen Receptor Modulators / Q000378:metabolism / Q000494:pharmacology; D013629:Tamoxifen / Q000378:metabolism / Q000494:pharmacology
chemical_list: D018931:Antineoplastic Agents, Hormonal; D003432:Cross-Linking Reagents; D004268:DNA-Binding Proteins; D004967:Estrogens; D008024:Ligands; D009363:Neoplasm Proteins; D011960:Receptors, Estrogen; D020845:Selective Estrogen Receptor Modulators; D013629:Tamoxifen