Divergent transcription occurs at the majority of RNA polymerase II (RNAPII) 
promoters in mouse embryonic stem cells (mESCs), and this activity correlates 
with CpG islands. Here we report the characterization of upstream antisense 
transcription in regions encoding transcription start site associated RNAs 
(TSSa-RNAs) at four divergent CpG island promoters: Isg20l1, Tcea1, Txn1, and 
Sf3b1. We find that upstream antisense RNAs (uaRNAs) have distinct capped 5' 
termini and heterogeneous nonpolyadenylated 3' ends. uaRNAs are short-lived with 
average half-lives of 18 minutes and are present at 1-4 copies per cell, 
approximately one RNA per DNA template. Exosome depletion stabilizes uaRNAs. 
These uaRNAs are probably initiation products because their capped termini 
correlate with peaks of paused RNAPII. The pausing factors NELF and DSIF are 
associated with these antisense polymerases and their sense partners. Knockdown 
of either NELF or DSIF results in an increase in the levels of uaRNAs. 
Consistent with P-TEFb controlling release from pausing, treatment with its 
inhibitor, flavopiridol, decreases uaRNA and nascent mRNA transcripts with 
similar kinetics. Finally, Isg20l1 induction reveals equivalent increases in 
transcriptional activity in sense and antisense directions. Together these data 
show divergent polymerases are regulated after P-TEFb recruitment with uaRNA 
levels controlled by the exosome.