title: Methods to Identify Chromatin-Bound Protein Complexes: From Genome-Wide to Locus-Specific Approaches.
abstract: High-throughput sequencing approaches coupled with functional genomics experiments have facilitated a rapid growth in our understanding of chromatin biology, from genome-wide maps of transcription factor binding and histone modifications to insights into higher order chromatin organization under specific cellular conditions. However in most cases these methods require a prior knowledge of the system of interest (e.g., targets for immunoprecipitation or modulation) and therefore are limited in their utility to identify novel components of pathways or for the study of uncharacterized pathways. Several orthologous proteomics approaches have been developed recently that bridge this gap, allowing the identification of protein complexes globally or at specific genomic loci. In this chapter the relative advantages of each approach will be explored and a detailed protocol given for DNA pull-down of a specific androgen receptor (AR) genomic target.
authors.affiliation: Li Ka Shing Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK. charlie.massie@cruk.cam.ac.uk.
authors.forename: Charles E
authors.initials: CE
authors.lastname: Massie
mesh_terms: D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D056426:Genetic Loci; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D011471:Prostatic Neoplasms / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D011944:Receptors, Androgen / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods; D014407:Tumor Cells, Cultured
chemical_list: C410798:AR protein, human; D002843:Chromatin; D011944:Receptors, Androgen
keywords: Androgen receptor (AR); Chromatin; Genomics; High-throughput screen; Nuclear hormone receptor; Prostate cancer; Proteomics; Transcription; Transcriptional regulation