Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms

The analysis of transgene silencing effects in plants and other eukaryotic organisms has revealed novel mechanisms of epigenetic regulation that are b ased on recognition of nucleic acid sequence homology. These homology-depen dent gene silencing phenomena are characterized by an inverse relationship between copy number of a particular sequence and expression levels. Dependi ng on whether promoter regions or transcribed sequences are repeated, silen cing occurs at the transcriptional or post-transcriptional level, respectiv ely. Different silencing effects involving DNA-DNA or RNA-DNA associations in the nucleus, and RNA-RNA interactions in the cytoplasm appear to reflect distinct host defense responses to parasitic sequences, including transpos able elements (TEs), viroids and RNA viruses. Natural epigenetic phenomena that resemble transgene silencing effects often involve endogenous genes co mprising recognizable TE sequences or rearrangements generated by TEs and c an thus be interpreted in terms of host defense systems. A genome defense t hat inactivates TEs by methylation might have been recruited during evoluti on to regulate the transcription of plant and vertebrate genes that contain remnants of TE insertions in promoter regions.