Gene regulation
Regulation can act through DNA accessibility, transcription factors, RNA processing or stability, translation, and protein activity. In bacteria, regulatory proteins can control several genes within an operon. Eukaryotic enhancers can influence promoters through DNA looping and protein interactions. Environmental signals may alter expression without changing DNA sequence. Chromatin changes often affect access, but a correlation between a mark and expression does not alone identify a mechanism.
If a nutrient binds a repressor and prevents it from binding an operator, genes previously blocked by that repressor can be transcribed. Track what the regulator actually does.
A liver cell does not become different from a neuron because it throws away the unused genes. Most such cells retain essentially the same genome.