  The ability of homologous chromosomes (or selected chromosomal loci) to pair
specifically in the apparent absence of DNA breakage and recombination
represents a prominent feature of eukaryotic biology. The mechanism of homology
recognition at the basis of such recombination-independent pairing has remained
elusive. A number of studies have supported the idea that sequence homology can
be sensed between intact DNA double helices in vivo. In particular, recent
analyses of the two silencing phenomena in fungi, known as repeat-induced point
mutation (RIP) and meiotic silencing by unpaired DNA (MSUD), have provided
genetic evidence for the existence of the direct homologous dsDNA-dsDNA
pairing. Both RIP and MSUD likely rely on the same search strategy, by which
dsDNA segments are matched as arrays of interspersed base-pair triplets. This
process is general and very efficient, yet it proceeds normally without the
RecA/Rad51/Dmc1 proteins. Further studies of RIP and MSUD may yield surprising
insights into the function of DNA in the cell.
