The development of high-throughput sequencing technologies dramatically accelerated the accumulation of data on genome structure, distribution of gene regulatory regions in the genome and specific features of their interaction. Technologies associated with chromatin immunoprecipitation are reviewed: ChIP-PET, ChIP-seq, and ChIA-PET. Computer-assisted methods for the analysis of transcription factor binding sites (TFBSs) and regulatory region structures throughout the genome are described. The paper demonstrates approaches to the solution of tasks related to genomic data annotation and identification of TFBSs and regulatory regions.