Similarities:

Comparisons between bacterial and RNA polymerase II have been performed.  Similarity in sequence has been shown between alpha, Rpb3, and Rpb11.  Alpha₂ binds beta to form a subcomplex that then binds beta’ that form the core enzyme.  Rpb3 and Rpb11 also form a subcomplex with Rpb2.  The Rpb3 and Rpb11 show the same fold as the alpha subunit in bacterial polymerase.  Beta and Rpb2 as well as beta’ and Rpb1 show sequence homology.  The pore in which RNA exits and where NTPs comes into the polymerase are conserved as well (4).

Differences:

Prokaryotes only contain three different promoter elements: -10, -35 promoters, and upstream elements.  Eukaryotes contain many different promoter elements: TATA box, initiator elements, downstream core promoter element, CAAT box, and the GC box to name a few.  Eukaryotes have three types of RNA polymerases, I, II, and III, and prokaryotes only have one type.  Eukaryotes form and initiation complex with the various transcription factors that dissociate after initiation is completed.  There is no such structure seen in prokaryotes.  Another main difference between the two is that transcription and translation occurs simultaneously in prokaryotes and in eukaryotes the RNA is first transcribed in the nucleus and then translated in the cytoplasm.  RNAs from eukaryotes undergo post-transcriptional modifications including: capping, polyadenylation, and splicing.  These events do not occur in prokaryotes.  mRNAs in prokaryotes tend to contain many different genes on a single mRNA meaning they are polycystronic.  Eukaryotes contain mRNAs that are monocystronic.  Termination in prokaryotes is done by either rho-dependent or rho-independent mechanisms.  In eukaryotes transcription is terminated by two elements: a poly(A) signal and a downstream terminator sequence (7).