In this review, we discuss regulatory elements of the eukaryotic genome that control transcription. We describe the functional anatomy of tissue specific promoters and promoters of house-keeping genes; current methodologies for prediction and identification of enhancers; the role of insulators in the enhancer-promoter communication and maintenance of the epigenetic status of genomic domains; and briefly discuss the relationship between the interphase chromatin topology and regulation of transcription. Considering these questions, we pay particular attention to the new data obtained in works on the high-throughput sequencing of primary transcripts and the genome-wide analysis of histone modifications.