Methylation of gene promoters or coding sequences is a common method of gene silencing and can be under genetic and/or epigenetic control. This is one of several mechanisms in how plants/animal/microbes manage gene expression. As you know, this is an exciting and emerging field in biology/genetics. The roles of micro-RNAs and transcription factors in regulating individual genes and/or whole metabolic pathways is now probably better understood in humans than in plants - but the principles are very similar. Rin is a classic transcription factor that regulates, directly or indirectly, several different processes in tomato fruit - together controlling the fruit ripening process. Methylation/silencing of specific genes may be involved - but not sure. The recessive loss-of-function mutant "rin" results in a non-ripening phenotype, as does alc/alc, but as noted in the photos above there are other phenotypic traits that are quite different between these two mutants - thus my interest.
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