*2.3. Modification Pattern*

As alien gene materials of the nuclear genome, NUPTs/NUMTs can cause host genome instability; they may lead to genomic region reshuffling, genome size expansion, and heterochromatization [16,38,48]. Epigenetic regulation, mainly including DNA methylation and histone tail modifications, provides a defense measure for inhibiting the activity of mobile DNA and other types of extraneous DNA [49,50].

The mutation patterns of NUPTs of a number of plant species show biased mutations of cytosine (C) → thymime (T) on one DNA strand, and guanine (G) → adenine (A) substitutions on the opposite strand [4,33,38,51]. These biased substitutions might be due to the hypermethylation of cytosine residues with subsequent deamination [52]. These observations suggest that DNA methylation might play essential roles in regulating integrated organellar DNAs, mainly associated with the transcription suppression of integrated organelle DNA [53,54]. In fact, it has been revealed that a considerable number of NUPTs are methylated, and the DNA methylation intensity and level decrease over evolutionary time. The DNA methylation-modified NUPTs may maintain the stability of plant nuclear genomes against the insertion of organellar DNA sequences and play an important role in the symbiosis of nuclear and organelle genomes [51]. Further methylome data analysis of epigenetic mutants in *Arabidopsis* and rice show that organellar DNA sequences are methylated mainly via the maintenance methylation machinery, involving *DDM1*, *CMT3*, *CMT2*, and *SUVH4*/*KYP*. However, other mechanisms, such as RNA-directed DNA methylation and homology-dependent DNA methylation machinery may also play roles in the methylation level.
