4.7 Article

Enhancer RNA profiling predicts transcription factor activity

Journal

GENOME RESEARCH
Volume 28, Issue 3, Pages 334-344

Publisher

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.225755.117

Keywords

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Funding

  1. National Science Foundation (NSF) IGERT grant [1144807]
  2. National Institutes of Health (NIH) [T32 GM008759]
  3. Boettcher Foundation's Webb-Waring Biomedical Research program
  4. Sie post-doctoral fellowship
  5. NSF [ABI DBI-12624L0]
  6. Division Of Graduate Education
  7. Direct For Education and Human Resources [1144807] Funding Source: National Science Foundation

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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.

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