We report the immediate effects of estrogen signaling on the transcriptome of 
breast cancer cells using global run-on and sequencing (GRO-seq). The data were 
analyzed using a new bioinformatic approach that allowed us to identify 
transcripts directly from the GRO-seq data. We found that estrogen signaling 
directly regulates a strikingly large fraction of the transcriptome in a rapid, 
robust, and unexpectedly transient manner. In addition to protein-coding genes, 
estrogen regulates the distribution and activity of all three RNA polymerases 
and virtually every class of noncoding RNA that has been described to date. We 
also identified a large number of previously undetected estrogen-regulated 
intergenic transcripts, many of which are found proximal to estrogen receptor 
binding sites. Collectively, our results provide the most comprehensive 
measurement of the primary and immediate estrogen effects to date and a resource 
for understanding rapid signal-dependent transcription in other systems.