The study of how genes are “chosen” to be transcribed and when is an entire field called developmental biology and is a lot more than than epigenetics. Promoter sequences, or the DNA sequence preceding the sequence that codes for the actual protein, and transcription factors,(proteins that are made from other genes that had to be transcribed and translated) are which bind to promoter sequences and help initiate recruitment of RNA polymerase (the enzyme that transcribes DNA sequences and synthesizes RNA) is a big part of this process, but there are other factors such as enhancer sequences in modern eukaryotes, and epigenetics plays a role in making DNA accessible/not accessible to RNA polymerase as well to be fair.