Controlling elements are wild cards in the epigenomic deck.

T he genomes of multicellular eukaryotes are loaded with retrotransposons, parasites that propagate by transcription of their genomes, reverse transcription, and insertion of a new copy into the host genome (1, 2). Waves of replication have formed families of mostly fragmentary or otherwise degenerate retroelements (1, 2). Epigenetic silencing suppresses retrotransposon activity, keeping them from wreaking genetic and epigenetic havoc in their hosts (3, 4), but active suppression must be maintained (2). Discussions of their biological role have focused on genetics: disruption of genomic structure, and adaptation to form regulatory elements and parts of proteins. Less obvious, but possibly far more important, is their ability to disrupt normal patterns of transcription. McClintock observed that DNA transposons in maize could reversibly alter the expression of genes in the general vicinity of their insertion sites, and so termed them ‘‘controlling elements’’ (5). Retrotransposons also have this ability: Depending on their epigenetic state, they may either lie quietly without interfering in affairs or seize control and dramatically change patterns of gene expression. In this issue of PNAS, Kano et al. (6) describe retrotransposon-controlling elements in the murine dactylin gene. Both appear to effect the dactylaplasia phenotype only when epigenetically active, and their activity is regulated by an unlinked modifier. This finding neatly illustrates some properties of controlling elements and promises in time to give new insights into the mechanisms by which they are kept silent (or not). Controlling elements create ‘‘transcriptional interference,’’ in which an inserted or reactivated promoter either alters the activity of a nearby promoter or itself transcribes a gene (7). Importantly, this property is separable from the purely genetic effects of an element’s insertion. The variety of their effects tells us something about how little we understand the mechanisms of gene regulation in complex genomes. Because controlling elements are epigenetically regulated, they may exhibit mosaic and heritable states of activity. Plant geneticists have developed a large body of work on controlling elements (5, 8), but two examples from animals are particularly well studied. In the murine agouti viable yellow (Avy) allele, an intracisternal A-particle (IAP) retrotransposon is inserted 100 kb upstream of agouti (Fig. 1A) (9). Agouti is normally expressed only in one phase of the hair follicle cycle; its product binds to melanocortin receptors and gives fur its agouti pattern (10). When silent, the IAP has little or no effect on the normal pattern of agouti expression, but when it is active, a cryptic promoter in its 5 LTR transcribes agouti in a constitutive pattern (9), producing a syndrome of yellow fur, obesity, type II diabetes, and cancer (10). Epigenetic mosaicism for activity of the IAP causes the phenotypes of isogenic Avy mice to vary from fully affected through a spectrum of mosaic intermediates to completely unaffected (11). The maternal epigenetic state of Avy is weakly heritable, indicating some tendency for germline stability, but a more prominent feature is germline epigenetic instability: Mice of any Avy phenotype will have offspring with a spectrum of phenotypes (11, 12). Thus, Avy mice illustrate key features of controlling elements: abrogation of normal transcriptional controls, epigenetic variation and inheritance, the requirement for an active transcription state, and the ability to act at a distance from the affected gene. The action of the IAP-controlling element on the agouti locus is simple: it transcribes agouti in a new pattern. The gypsy retrotransposon of Drosophila has a more complex mode of action. Gypsy is an LTR retrotransposon; when inserted 5 of yellow, it blocks the action of upstream enhancers on the yellow promoter (Fig. 1B) (13). It has similar effects in other loci (14) and may also