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Liver X receptors are members of the nuclear receptor superfamily of transcription factors. The LXR genes (NR1H2 and NR1H3) encode for two different proteins referred to as LXRα and LXRβ. Each LXR presents diverse tissue distribution but similar target DNA-binding elements and ligands. Both LXRs act as relevant transcriptional regulators of cholesterol metabolism in many tissues. Additionally, LXRs participate in innate immunity and inflammation. Therefore, in order to understand the molecular requirements that operate in LXR-dependent transcription, it is important to decipher LXR genomic binding properties. We have recently performed genome-wide binding analysis of LXR proteins. In this method paper, we describe a detailed computational protocol primarily based on HOMER software package for the analysis of ChIP-seq data.
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