CHROMOMETHYLTRANSFERASE3/KRYPTONITE maintains the sulfurea paramutation in Solanum lycopersicum

Paramutation involves the transfer of a repressive epigenetic mark from a silent allele to an active homolog and, consequently, non-Mendelian inheritance. In tomato, the sulfurea (sulf) paramutation is associated with a high level of CHG hypermethylation in a region overlapping with the transcription start site (TSS) of the SlTAB2 gene that affects chlorophyll synthesis. The CCG subcontext hypermethylation is underrepresented at this region relative to CTG or CAG, implicating the CHROMOMETHYLTRANSFERASE3a (CMT3) in paramutation at this locus. Consistent with this interpretation, loss of CMT3 function leads to loss of the sulfchlorosis, the associated CHG hypermethylation, and paramutation. Loss of KRYPTONITE (KYP) histone methyltransferase function has a similar effect linked to reduced H3K9me2 at the promoter region of SlTAB2 and a shift in higher order chromatin structure at this locus. Mutation of the largest subunit of RNA polymerase V (PolV) in contrast does not affect sulf paramutation. These findings indicate the involvement of a CMT3/KYP-dependent feedback loop rather than the PolV-dependent pathway leading to RNA-directed DNA methylation (RdDM) in the maintenance of paramutation.