Control of DNA excision efficiency in Paramecium

Programmed excision of internal eliminated sequences (IESs) occurs at thousands of sites in ciliate genomes. How this is controlled is largely unknown. Here, we report the characterization of the non-efficiently excised 156ψG-11 IES from Paramecium primaurelia strain 156 and that of the efficiently excised 168ψG-11 IES, an allelic variant from strain 168. Then, we report a genetic and molecular analysis of IES excision efficiency in F(1) progeny derived from interstrain crosses and in F(2) homozygous progeny derived from F(1) autogamy. IES 168ψG-11 excision efficiency was ∼100% in all cases. IES 156ψG-11 excision efficiency was 19 ± 13% in F(1) progeny and 0.6 ± 1.1% in F(2) progeny. No trans-excision event between IESs 156ψG-11 and 168ψG-11 was detected within the F(1) progeny. These data demonstrate that the excision efficiency of this IES is variable and controlled by a cis-acting element. This should encompass positions 8 and/or 9 of the right IES end, which display allele differences. Finally, the 30-fold stimulation of IES 156ψG-11 excision efficiency within F(1) progeny relative to F(2) progeny demonstrates that Paramecium IES excision efficiency is sensitive either to a conjugation-specific trans-acting factor provided by the zygotic genome, or to homologous chromosome cross-talk.