RT Journal
A1 Azofeifa, Joseph G.
A1 Allen, Mary A.
A1 Hendrix, Josephina R.
A1 Read, Timothy
A1 Rubin, Jonathan D.
A1 Dowell, Robin D.
T1 Enhancer RNA profiling predicts transcription factor activity
JF Genome Research 
JO Genome Research 
YR 2018 
FD March 01 
VO 28 
IS 3 
SP 334 
OP 344 
DO 10.1101/gr.225755.117 
UL http://genome.cshlp.org/content/28/3/334.abstract 
AB Transcription factors (TFs) exert their regulatory influence through the binding of enhancers, resulting in coordination of gene expression programs. Active enhancers are often characterized by the presence of short, unstable transcripts termed enhancer RNAs (eRNAs). While their function remains unclear, we demonstrate that eRNAs are a powerful readout of TF activity. We infer sites of eRNA origination across hundreds of publicly available nascent transcription data sets and show that eRNAs initiate from sites of TF binding. By quantifying the colocalization of TF binding motif instances and eRNA origins, we derive a simple statistic capable of inferring TF activity. In doing so, we uncover dozens of previously unexplored links between diverse stimuli and the TFs they affect.