There are a whole bunch of signaling pathways that ultimately let the cell ‘know’ which parts of the DNA should be transcribed and when. The chromosomes are normally folded up tight, around proteins called histones. These and other proteins can be in the way enough that genes can’t be transcribed, but they can be moved out of the way. There are other proteins or RNA molecules that can bind to the DNA, that can either block some genes, or cause others to be transcribed more. The DNA itself can be modified in ways that determine if it can be transcribed
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