We would also expect heterozygotes or heterogeneous genotypes at some loci in this case.
If so, we would expect heterozygous or heterogeneous genotypes at some loci or mixtures of plastid types within populations.
In addition, two non-redundant forms of a nuclear RNA polymerase IV (specific to plants), namely Pol IVa and Pol IVb, are also required at some loci.
Although RDR2 may be unnecessary as a polymerase subunit at some loci like inverted repeats, it still contributes to the formation or stability of a complex that contains active DCL3 [8].
However, the DNA methyltransferase CHROMOMETHYLASE3 (CMT3) also plays some role in CHH maintenance and acts redundantly with DRM2 at some loci [11].
Chromatin modification may occur as a consequence of AID activity to promote mutagenesis at some loci, or histone monoubiquitinations could help recruit AID.
However, there were some differences between species at some loci, e.g., ssrQpZAG15, ssrQpZAG110, quru-GA-0C11, ssrQrZand7, and ssrQrZAG112 (Table 3).
CMT3 is also the main enzyme acting to maintain CHG methylation throughout the genome, however, at some loci DRM2 also plays an important role [11], [32].
The colony used in this study does not harbor the chromosomal rearrangements segregating in natural populations, but small and/or unknown inversions may be present and could play a role in preserving genetic variation at some loci.
We have previously reported that at some loci (but not at others) gene-wide histone H3 acetylation leads to efficient AR-mediated transcription in C4-2B but not in LNCaP cells [24].
Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects.
