In hypotrichous ciliates, all of the macronuclear DNA is in the form of low molecular weight molecules with an average size of -2200 base pairs. Total macronuclear DNA from four hypotrichs has been shown to have inverted terminal repeats by direct sequence analysis. In Oxytricha nova, Oxytricha sp., and Stylonychia pustulata, this terminal sequence may be written as 5'-C4A4C4A4C4 ... 3'-G4T4G4T4G4T4G4T4G4 ...In Euplotes aediculatus, the sequence is similar but differs in the lengths of the duplex region (28 base pairs) and of the putative 3' extension (14 base pairs). Also in Euplotes, a second common sequence of 5 base pairs (A:T:G-A-A) occurs internal to the terminal repeat and a 17-base-pair heterogeneous region:The length of the terminal repeat sequence for 0. nova was confirmed in cloned macronuclear DNA molecules.Ciliated protozoa of the order Hypotrichida have two types of nuclei-a small transcriptionally inactive (germinal) micronucleus and a large DNA-rich macronucleus, which contains the entire functional vegetative genome. Whereas the DNA of the micronucleus is large (>>150 X 10' daltons) and is contained in chromosomes, the transcriptionally active macronuclear genome is achromosomal; the DNA exists as a heterogeneous distribution of molecules ranging in size from 400 to ==20,000 base pairs (bp) with an average of 2200 bp (1, 2).The macronucleus is formed de novo from a diploid micronucleus after sexual conjugation. In brief, formation of the macronucleus involves the polytenization of micronuclear chromosomes, followed by fragmentation of polytene chromosomes at interbands and degradation of --95% of the DNA. The degradation phase eliminates all detectable repetitive DNA and most of the unique sequence DNA. What remains are small DNA molecules, which are extensively replicated to form the mature macronuclear genome (for review, see ref.3).This subset of the micronuclear DNA sequences that is retained in the macronucleus contains all of the genetic information (except for mitochondrial) for vegetative growth.The macronucleus contains --24,000 different DNA sequences, present at an average of 1000 copies per macronucleus. Each of these gene-sized molecules is a separate functional genetic unit. Denaturation of macronuclear DNA followed by a short period of reassociation leads to formation of singlestranded circles in more than 80% ofthe molecules as observed by electron microscopy. The single-stranded DNA is held in a circular configuration by a short duplex region. Therefore, all or nearly all of the gene-sized molecules of the macronucleus have an inverted terminal repeat (4). The sequence of this terminal repeat was shown to be the same in many ofthe molecules (5), although the sequence reported for the terminal repeat was not correct. We report here the correct sequence and show that the sequence forming the inverted terminal repeat is almost the same in four different hypotrich species. To establish the structure of the termini of native DNA molecules, we determined both the 3'-and 5'-en...

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The germline genomes of ciliated protozoa are dynamic structures, undergoing massive DNA rearrangement during the formation of a functional macronucleus. Macronuclear development involves chromosome fragmentation coupled with de novo telomere synthesis, numerous DNA splicing events that remove internal segments of DNA, and, in some ciliates, the reordering of scrambled gene segments. Despite the fact that all ciliates share similar forms of DNA rearrangement, there appears to be great diversity in both the nature of the rearranged DNA and the molecular mechanisms involved. Epigenetic effects on rearrangement have also been observed, and recent work suggests that chromatin differentiation plays a role in specifying DNA segments either for rearrangement or for elimination.

During the formation of a transcriptionally active macronucleus, ciliated protozoa excise large numbers of interstitial segments of DNA (internal eliminated sequences; IESs) from their chromosomes. In this study we analyze the published sequences of 20 IESs that interrupt surface protein genes of Paramecium and identify a consensus inverted terminal repeat. This sequence is similar to the ends of the Tc1-related transposons found in nematodes and other metazoans, as well as to both the ends of the Tec transposons and at least some of the IESs in the distantly related ciliate Euplotes crassus. The results of these analyses bolster previous proposals that IESs were created by transposition.