Nuclear receptor location analyses in mammalian genomes: from gene regulation to regulatory networks

Rapid progress in mapping nuclear receptor binding sites, referred to as "location analysis," has recently been achieved through the use of chromatin immunoprecipitation approaches. Location analysis can be performed on a single locus or cover a complete genome, and the resulting datasets can be probed to identify direct target genes and/or investigate the molecular mechanisms by which nuclear receptors control gene expression. In addition, when coupled with other genetic and functional genomics investigative methods, location analysis has proven to be a powerful tool with which to identify novel biological functions of nuclear receptors and build transcriptional regulatory networks. Thus, the knowledge gained from several recent chromatin immunoprecipitation-based studies has challenged basic concepts of nuclear receptor action, offered new insights into gene-regulatory mechanisms, and led to the identification of nuclear receptor-controlled biological functions.