There are a number of proteins involved in termination of transcription, particularly a protein called rho. However the mechanism by which rho terminates transcription is not understood, and there are as yet no apparent sequence similarities in these rho-dependent termination regions.
Figure 1: A rho-independent method of transcription termination.
The direction of transcription is from left to right, the RNA polymerase
encounters a G-C rich inverted repeat which forms a hairpin loop, causeing
the RNA polymerase to pause. The DNA reanneals, knocking off the RNA
polymerase and the newly synthesised chain.
There is a rho-independent method of termination which is understood,
(depicted in figure 1, page 
)
in which the RNA polymerase reaches a GC rich region with an inverted
repeat - such as 
CCCACT
AGTGGG
. When such a feature
is encountered, the newly-synthesised RNA forms a hairpin loop and it
is believed that this may cause the polymerase to pause, allowing
the DNA to reanneal locally and breaking off the synthesised RNA chain.
This is associated in particular with a sequence of U's in the RNA, the
A-U bonds being weaker than G-C (2, as opposed to 3 hydrogen bonds), making
it more likely for the RNA to break off.