Regulation of gene expression in prokaryotes occur at the promoter level. Repression happens because of the Operator Repressor interactions. Similarly what part of the DNA replaces the function of operators in eukaryotes?
What is the repressor binding site of eukaryotic genome called as?
I agree with Artur, I would like to add, that the epgienetic repressor mechanism that exists in eukaryotes specifically is the nucleosome positioning around promoters. By and large, the rule can be - that when bound to Nucleosomes - the DNA becomes inaccessible to activating transcription factors. therefore positioned nulceosomes on Promoters serve the scaffold repressor function that needs to be undone by activators and chromatin remodelors. The field of epigenetics has several other mechanisms that explain activation and repression from a unique angle.
another point to keep in mind is that transcriptional repression occurs through mutual interaction of a different regulatory complexes. of those just a minor part binds directly the DNA, while all the others are needed to maintain the chromatin status (i.e. histone mods) in a permissive/repressive state. we should not view anymore transcriptional regulation as one protein -> one binding site -> one effect...cells have to be seen and interpreted as a system and the combination of epigenetic modifications (as mentioned above), coregulatory complexes and transcription factors binding then leads to the "final" transcriptional effect. if you have a specific coregulatory protein in mind there are databases that show if/where this binds. a great list was posted on SeqAnswer here: http://seqanswers.com/forums/showthread.php?t=27484
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