GSE18643
Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II
We developed a novel approach to isolate and characterize, at nucleotide-level resolution, the RNAs derived from RNA polymerase II (Pol II) in early elongation complexes. We find that high numbers of these short RNAs are not correlated with gene expression but instead are indicative of promoter-proximally stalled polymerase. High amounts of these short RNAs are generated from more than one third of all genes, indicating that Pol II  stalls in the promoter-proximal region on  global scale. We also find that the nucleotide composition of the initially transcribed sequence plays an important role in promoting transcriptional stalling and that early elongation complexes are highly susceptible to backtracking and arrest. Overall design: Global analysis of RNAs produced by promoter-proximal Pol II.