Genome-wide rearrangements of dna in ciliates

This chapter provides an update of the molecular analysis in DNA rearrangements. Sufficient progress has been made to provide good insights into their regulatory mechanisms and allow meaningful speculations on their relationships to other DNA rearrangement processes. The chapter focuses on the studies of the two processes (chromosome fragmentation and internal DNA deletion), which also occur, but separately, in nematodes (chromosome fragmentation) and crustaceans (DNA deletion). These processes are described briefly to complete the picture of DNA rearrangements in ciliates. The chapter discusses the unusual epigenetic effects on chromosome breakage and DNA deletion, and is concluded by offering the authors' views on the possible functions of these processes. The degree of fragmentation in the oligohymenophorans such as Tetrahymena, Paramecium, and Glaucoma is nearly two orders of magnitude lower than in the hypotrichous ciliates. The differences in the chromosome fragmentation process are quite extensive among the ciliates studied. Even in Tetrahymena and Euplotes, for which sequences controlling breakage have been identified, there is little evidence that they share a common mechanism of fragmentation. Site-specific deletion of DNA sequences, like chromosome fragmentation, occurs in all ciliates examined, but its extent varies greatly among species. In Paramecium, the study of internal eliminated sequences (IESs) started much later than in other ciliates, but a few dozen IESs have already been sequenced in this organism.