Functional studies of large transcription units, clustered genes and c
hromosomal loci require the design of novel experimental toots to engi
neer genomic macro-rearrangements. Here, we present a strategy to prod
uce deficiencies or duplications by crossing mice carrying loxP sites
in homologous loci. This trans-allelic targeted meiotic recombination
(TAMERE) protocol allows for the combination of various alleles within
a particular locus as well as for generation of interchromosomal uneq
ual exchanges. Novel genetic configurations can thus be produced witho
ut multiple targeting and selection steps in embryonic stem (ES) cells
. A concomitant deletion/duplication event of the Hoxd12 locus shows t
he potential of this approach. The high frequency of such targeted exc
hanges in vivo makes TAMERE a powerful genetic tool applicable to rese
arch areas in which complex genomic modifications are required.