Even though bacteria and eukaryotes have many similarities in the logic of gene regulation, there are some fundamental dissimilarity in the underlying mechanisms and machinery. Both the bacteria and eukaryotes use sequence specific DNA binding proteins, but eukaryotic genomes are bigger than prokaryotic genomes. Thus, regulation of eukaryotic genomes has become more complex.
The main difference between the bacterial genome and eukaryotic genome is that eukaryotic genome is packaged into nucleosomes, forming chromatin, while bacterial genome lacks them. Thus, chromatin structure is dynamic and it plays an essential role in eukaryotic gene regulation.
Bacterial genome being simple in structure, it will be in “on” mode always. This let the RNA polymerase to bind to the promoter easily, when there are no other regulatory proteins around to bind to the DNA. Thus, transcription initiation will be prevented if binding of RNA polymerase is blocked.
In contrast, eukaryotic genome being very complex in structure, it will not allow RNA polymerase to bind so easily. As a result, it needs other regulatory proteins such as activator regulatory proteins. The structure of the chromatin should be changed in order to activate transcription in eukaryotes.
Thus, the state of genes in bacteria with respect to gene activation is “on”, and it is “off” in eukaryotes.