**5. Mechanisms of Organellar DNA Integration**

Organellar DNA sequences can be transferred to the nucleus through two distinct pathways, namely, direct DNA integration [89] and RNA-mediated DNA transfer via reverse transcription. Some experimental and bioinformatics studies suggest that many NUPTs/NUMTs are very large and include intergenic and/or non-coding regions of organellar DNA [11,37,38,89,90]. Thus, the migration of organellar DNA fragments into the nucleus may be mediated by DNA. However, the functional organellar gene relocated to the nuclear genome with splicing and RNA editing, and this event seems to have occurred before transfer; this phenomenon suggests the involvement of RNA intermediates [91–93]. Thus, the two pathways may both have important roles to play in the transfer process.

DNA escapes from organelles and its incorporation into the nucleus has been experimentally investigated in yeast [58,79] and tobacco [10,12]. Bioinformatics analysis and direct experimental evidence suggest that nonhomologous end-joining mechanism (NHEJ) is involved in organellar DNA incorporation during double-stranded break (DSB) repair. In yeast, fragments of mitochondrial DNA segments are captured into DSBs in the nuclear genome during the DSB healing process via NHEJ [79,94]. DSBs can be induced in vivo by exogenous and endogenous factors; they are the most potentially deleterious type of DNA damage [95–97]. DSBs can be usually repaired via the insertion of filler DNA into the lesion, whereas organellar DNA can be passively used as the filler DNA. The integration includes two DSB repair events, which are mediated by the short sequence microhomology (1–7 bp, "micro-identities") between the break chromosome ends and organellar DNA or by a blunt-end repair without homology [79,94,96,98]. A similar mechanism involving NHEJ at DSB sites was examined in tobacco [45,55,62]. The integrated fragments are usually complicated mixtures of multiple different segments of chloroplast DNA end joined together based on sequence microhomology [62]. These results suggested that linking of linear DNA fragments generates chimeric DNA molecules before or during insertion into the nuclear genome [38,62]. Sequence analysis revealed that such terminal micro-identities have also been presented for NUMT integrants in humans [99,100], indicating that organellar fragments integrating into the nuclear genome via NHEJ during DSB repair process might be a common mechanism conserved in eukaryotic organisms. A recent study has shown that several mosaic organellar integrants present signatures of long homology; thus, other mechanisms, such as homologous recombination may also contribute to organellar DNA integration [40].
