One fundamental difference between gene regulation in prokaryotes and eukaryotes is that prokaryotes often use operons to organize their genes, while eukaryotes generally do not. Prokaryotic operons allow for the coordinated expression of genes that are functionally related, facilitating a quicker response to environmental changes. In contrast, eukaryotic genes are typically controlled individually and often involve more complex regulatory mechanisms, including enhancers and silencers, as well as post-transcriptional modifications.
So the correct statement from the options provided would be that all eukaryotes use operons to organize their genes while prokaryotes do not. However, please note this statement is incorrect because actually, it is the other way around: prokaryotes use operons, while eukaryotes do not.
The option "Prokaryotes do not store their genes in a nucleus like eukaryotes do" highlights a difference as well; prokaryotes have their genetic material in a nucleoid region without a membrane-bound nucleus, while eukaryotes have a defined nucleus.
Thus, in reviewing the statements, the best choice would be that "Prokaryotes do not store their genes in a nucleus like eukaryotes do," as it is factually accurate.