Termination is part of the process of transcribing RNA. In eukaryotes, a termination factor is required to release the newly made (nascent) RNA from the transcription complex. Prokaryote mRNAs often do not require a termination factor: an inverted repeat followed by a string of Us (uracils) in the mRNA template strand forms a stem-loop structure which destabilizes binding by the RNA polymerase and causes Rho-independent transcription termination.
The most extensively studied transcriptional termination factor is the Rho protein of E. coli. The Rho protein recognizes a cytosine-rich region of the elongating mRNA, but the exact features of the recognized sequences remain unknown. Rho forms a ring-shaped hexamer and advances along the mRNA, hydrolyzing ATP, toward RNA polymerase (5' to 3' with respect to the mRNA). When the Rho protein reaches the RNA polymerase complex, transcription is terminated by dissociation of the RNA polymerase from the DNA. The structure, as well as the activity, of the Rho protein is similar to that of the F1 subunit of ATP synthase, supporting the theory that the two share an evolutionary link. The antibiotic bicyclomycin works by inhibiting Rho.
The process of transcriptional termination is less well understood in eukaryotes, which have extensive post-transcriptional RNA processing. Each of the three types of eukaryotic RNA polymerase has a different termination system. Eukaryotic termination factors bind to the termination signal region and disturb RNA polymerase II as it moves by, causing it to fall off the DNA strand within the next 300 base pairs. This 300 bp region is removed during processing, before poly(A)tailing (see Polyadenylation).