The termination of transcription in eukaryotic genes is less well understood than in bacterial genes. The three eukaryotic RNA polymerases use different mechanisms for termination. RNA polymerase I requires a termination factor, like the rho factor utilized in termination of some bacterial genes. Unlike rho, which binds to the newly transcribed RNA molecule, the termination factor for RNA polymerase I binds to a DNA sequence downstream of the termination site.

RNA polymerase III ends transcription after transcribing a terminator sequence that produces a string of Us in the RNA molecule, like that produced by the rho-independent terminators of bacteria. Unlike rho-independent terminators in bacterial cells, RNA polymerase III does not requre that a hairpin structure precede the string of Us.

In many of the genes transcribed by RNA polymerase II, transcription can end at multiple sites located within a span of hundreds or thousands of base pairs. As we will see in Chapter 14, the transcription of these genes continues well beyond the coding sequence necessary to produce the mRNA. After transcription, the 3' end of pre-mRNA is cleaved at a specific site, designated by a consensus sequence, producing the mature mRNA. Research findings suggest that termination is coupled to cleavage, which is carried out by a cleavage complex that probably associates with the RNA polymerase. This complex may suppress termination until the consensus sequence that marks the cleavage site is encountered. The 3' end of the pre-mRNA is then cleaved by the complex, and transcription is terminated downstream.

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