Genome sequencing in human and other organisms make it possible to map and analyze the regulatory elements of the genome. Yet there are only scarce experimental data on mapping regulatory elements, such as enhancers, silencers, insulators, transcription terminators, and replication origins, especially at the level of the whole genome. In silico prediction of the positions of such elements is rather difficult because their functions are often tissue-or cell-specific. Hence, it is important to develop high-throughput experimental approaches to the identification and mapping of the functional elements of the genome. The review considers such approaches developed for mammalian genomes, as the identification of their regulatory elements is essential for complete functional genome annotation. © 2007 Pleiades Publishing, Inc.