Chromosome end formation and internal sequence elimination as alternative genomic rearrangements in the ciliate Paramecium.

Programmed chromosome end formation resulting from DNA fragmentation and telomeric repeat addition as well as programmed internal sequence elimination occur extensively during differentiation of macronuclear genomes from micronuclear chromosomal sets in ciliated protozoa. Major macronuclear telomere addition sites were previously identified some 5 kb downstream from the G gene that encodes the G surface antigen in Paramecium primaurelia strain 156. Here I report the existence of minor telomeric addition sites some 2.8 kb downstream from the G gene. I show that major and minor macronuclear chromosomal ends arise by micronuclear DNA fragmentation, since none of them matches a micronuclear chromosomal end. Three DNA segments absent from the previously established macronuclear sequence map around the minor fragmentation sites in the micronuclear DNA. I show that one of these internal eliminated sequences is retained on some macronuclear chromosome copies and that all retained copies are found at minor telomeres. These results suggest that chromosome fragmentation and internal sequence elimination are alternative outcomes of a single DNA processing pathway.