TY  - JOUR
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
Y1  - 2018/03/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 334 
EP  - 344 
DO  - 10.1101/gr.225755.117 
VL  - 28 
IS  - 3 
UR  - http://genome.cshlp.org/content/28/3/334.abstract 
N2  - 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. 
ER  -