Position-effect variegation in Drosophila is the mosaic expression of a gene juxtaposed to heterochromatin by chromosome rearrangement. The brown (bw +) gene is unusual in that variegating mutations are dominant, causing "trans-inactivation" of the homologous allele. We show that copies of bw + transposed to ectopic sites are not trans-inactivated by rearrangements affecting the endogenous gene. However, when position-effect variegation is induced on an ectopic copy by chromosome rearrangement, the allele on its paired homolog is trans-inactivated, whereas other copies of bw + are not. This confirms that trans-inactivation is "chromosome local" and maps the responsive element to the immediate vicinity of brown. Subsequent P-transposase-induced deletions within the ectopic copy in cis to the rearrangement breakpoint caused partial suppression of trans-inactivation. Surprisingly, the amount of suppression was correlated with deletion size, with some degree of trans-inactivation persisting even when the P[bw +] transposon was completely excised. The chromosome-local nature of the phenomenon and its extreme sensitivity to small disruptions of somatic pairing leads to a model in which a regulator of the brown gene is inactivated by direct contact with heterochromatic proteins.[Key Words: Position-effect variegation; Drosophila; somatic pairing; in vivo deletion mappingl Received November 21, 1990; accepted December 18, 1990.A common class of mutations induced by ionizing radiation in Drosophila are the variegating position effects. These are generally caused by chromosomal rearrangements placing euchromatic genes in the vicinity of heterochromatin, the compacted regions of chromosomes that remain condensed during most of the cell cycle (for review, see Spofford 1976; Henikoff 1990). The variegated phenotype is caused by reduction in gene expression in some cells but not in others, evidently as a result of transcriptional inactivation (Henikoff 1981;Rushlow et al. 1984;Henikoff and Dreesen 1989). Consistent with this interpretation, position-effect variegation of nearly all genes is recessive, implying that inactivation of one copy of a gene in cis has no effect on the copy in trans. However, variegated position effects on a few genes, including the brown (bw +) gene, are dominant (Muller 1932;Slatis 1955;Stem and Kodani 1955;Henikoff 1979;O'Donnell et al. 1989).Recently, we showed that dominant position-effect variegation of brown involves a sharp reduction in mRNA accumulation from both copies of the gene, the copy in cis to the rearrangement breakpoint (cis-inactivation) and the copy in trans (trans-inactivation). We proposed a somatic pairing model in which the brown gene region, inactivated by virtue of its juxtaposition to heterochromatin, could transmit the inactivated state to the copy of brown in trans. Evidence for this model was the sensitivity of trans-inactivation to chromosome configurations that are expected to disrupt somatic pairing in the vicinity of the brown gene.The somatic pairing model makes sev...