Environment and structure of chromatin underlie epigenetics, and they also facilitate transcriptional regulations by nuclear receptors including VDR. In this short review, the molecular basis of chromatin remodeling and post-translational modifications of histone proteins are illustrated with characterization of their regulators, providing mechanisms for co-regulation of epigenetics and transcription on chromatin. Moreover, the role of enhancer RNA (eRNA), one of the non-coding RNAs, in chromatin configuration is discussed for gene regulation by VDR.