The carboxyl-terminal domain (CTD) of RNA polymerase II (Pol II) can be 
phosphorylated at serine 2 (Ser-2) and serine 5 (Ser-5) of the CTD heptad repeat 
YSPTSPS, and this phosphorylation is important in coupling transcription to RNA 
processing, including 5' capping, splicing, and polyadenylation. The mammalian 
endogenous dihydrofolate reductase and gamma-actin genes have been used to study 
the association of Pol II with different regions of transcribed genes 
(promoter-proximal compared to distal regions) and the phosphorylation status of 
its CTD. For both genes, Pol II is more concentrated in the promoter-proximal 
regions than in the interior regions. Moreover, different phosphorylation forms 
of Pol II are associated with distinct regions. Ser-5 phosphorylation of Pol II 
is concentrated near the promoter, while Ser-2 phosphorylation is observed 
throughout the gene. These results suggest that the accumulation of paused Pol 
II in promoter-proximal regions may be a common feature of gene regulation in 
mammalian cells.