Epigenetic regulation of Mammalian genomes by transposable elements

Transposable element (TE) sequences make up a substantial fraction of mammalian genomes and exert a variety of regulatory influences on mammalian genes. We explore the contributions of TEs to the epigenetic mechanisms that regulate mammalian genomes, emphasizing nucleosome positioning and epigenetic histone modifications. A link between TEs and epigenetics rests on the fact that underlying genetic sequences partially mediate the nature and identity of epigenetic modifications. Here, we review the studies that have uncovered histone modifications that are targeted to mammalian TE sequences and propose a series of hypotheses regarding the potential epigenetic regulatory effects of mammalian TEs. We propose that mammalian TE sequences have specific nucleosome binding properties with regulatory implications for nearby genes, are involved in the phasing of nucleosomes, and recruit epigenetic modifications to function as enhancers; that epigenetic modifications at TE sequences affect the regulation of nearby genes; and that TEs serve as epigenetic boundary elements. It is hoped that these proposed scenarios may help to serve as a roadmap for future investigations into the epigenetic regulatory effects of mammalian TEs.