A DNA replication-arrest site RTS1 regulates imprinting by determining thedirection of replication at mat1 in S-pombe

Mating-type switching in Schizosaccharomyces pombe involves a strand-specif ic, alkali-labile imprint at the mat1 (mating-type) locus. The imprint is s ynthesized during replication in a swi1, swi3, and polyinerase alpha (swi7) dependent manner and is dependent on mat1 being replicated in a specific d irection. Here we show that the direction of replication at mat1 is control led by a cis-acting polar terminator of replication (RTS1). Two-dimensional gel analysis of replication intermediates reveals that RTS1 only terminate s replication forks moving in the centromere-distal direction. A genetic an alysis shows that RTS1 optimizes the imprinting process. Transposing the RT S1 element to the distal side of mat1 abolishes imprinting of the native ma t1 allele but restores imprinting of an otherwise unimprinted inverted mat1 allele. These data provide conclusive evidence for the "direction of repli cation model" that explains the asymmetrical switching pattern of S. pombe, and identify a DNA replication-arrest element implicated in a developmenta l process. Such elements could play a more general role during development and differentiation in higher eukaryotes by regulating the direction of DNA replication at key loci.