Many features of gene regulation are common to both bacterial and eukaryotic cells. For example, in both types of cells, DNA-binding proteins influence the ability of RNA polymerase to initiate transcription. However, there are also some differences. First, many prokaryotic genes are organized into operons and are transcribed into a single RNA molecule. Although some operon-like gene clusters have been found in worms and even some primitive chordates, most eukaryotic genes have their own promoters and are transcribed separately. Second, chromatin structure affects gene expression in eukaryotic cells: DNA must partly unwind from the histone proteins before transcription can take place. Finally, the presence of the nuclear membrane in eukaryotic cells separates transcription and translation in time and space. Therefore, the regulation of gene expression in eukaryotic cells is characterized by a greater diversity of mechanisms that act at different points in the transfer of information from DNA to protein.

Eukaryotic gene regulation is less well understood than bacterial gene regulation, partly owing to the larger genomes of eukaryotes, their greater sequence complexity, and the difficulty of isolating and manipulating mutations that can be used in the study of gene regulation. Nevertheless, great advances in our understanding of the regulation of eukaryotic genes have been made in recent years.