(a) Cointegrate transposition. Single stranded cuts are made by transposase at both ends of the transposon (black, striped box) in donor DNA (black). The 3′ hydroxyl ends of the transposon are ligated to 5′‐phosphates of transposase‐cleaved target DNA. DNA replication fills single‐stranded gaps and recombination between duplicated transposon sequences separates the molecules yielding a donor site that retains the transposon and a target site that has acquired the transposon. (b) ‘Cut and paste’ transposition. Donor DNA (black) is cleaved at both ends of the transposition (striped black box) by transposase. The 3′ hydroxyl of the transposon is ligated to the transposase‐liberated 5′‐phosphate groups of the target DNA (red). The end result is a transposon inserted into target DNA and a double‐strand break (DSB) at the donor locus.

V‐J joining. The product of V‐J joining is an imprecise coding joint encoding part of an immunoglobulin G (IgG) molecule, and a precisely joined signal joint that is eventually degraded. DNA‐PK, DNA‐dependent protein kinase; RSS, recombination signal sequence.

Nonreciprocal gene conversion of an internal VSG gene (D) into an active telomeric expression site. The expressed VSG gene is located downstream of 76‐bp repeats and the eight expression site‐associated genes (ESAGs). The ESAGs are not affected in this case but may be by telomeric recombination and in situ switches. X, 76‐bp repeats; boxes A–E, distinct VSG genes, black stripes in A–E, conserved 3′ region.

(a) Organization of DNA at the micronuclear and macronuclear loci of the ARP1 gene of Tetrahymena thermophila. The area inside the diagonal lines indicates micronucleus‐specific DNA whereas outside these lines macronuclear and micronuclear sequences are identical. The 2.9‐kb eliminated sequence between the diagonal lines is named the micronucleus‐specific element (mse2.9). The eliminated sequence is situated within the second intron of ARP1. Exons are marked by clear boxes; introns by shaded boxes. E, EcoRI; H, HindIII; X, XbaI. (b) Model of IES (internal eliminated sequence) deletion in T. thermophila. Red arrows represent DNA cleavage; green arrows indicate junctions created by IES excision. IES excision is initiated by a staggered double‐strand break produced at a site defined by properly situated adenosine residues on either strand. A one‐step transesterification reaction occurs to produce the chromosomal junction on one strand. Processing of the intermediate occurs to yield the mature junction. Reproduced with permission from Saveliev SV and Cox MM (1995) Genes and Development9: 248–255.