In the cell, RNA polymerase II (pol II) efficiently transcribes DNA packaged 
into nucleosomes, but in vitro encounters with the nucleosomes induce catalytic 
inactivation (arrest) of the pol II core enzyme. To determine potential 
mechanisms making nucleosomes transparent to transcription in vivo, we analyzed 
the nature of the nucleosome-induced arrest. We found that the arrests have been 
detected mostly at positions of strong intrinsic pause sites of DNA. The 
transient pausing makes pol II vulnerable to arrest, which involves backtracking 
of the elongation complex for a considerable distance on DNA. The histone-DNA 
contacts reestablished in front of pol II stabilize backtracked conformation of 
the polymerase. In agreement with this mechanism, blocking of backtracking 
prevents nucleosome-induced arrest. Transcript cleavage factor TFIIS reactivates 
the backtracked complexes and promotes pol II transcription through the 
nucleosome. Our findings establish the crucial role of elongation factors that 
suppress pol II pausing and backtracking for transcription in the context of 
chromatin.