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Enhancer RNA profiling predicts transcription factor activity

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 unc...

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Detalles Bibliográficos
Autores principales: Azofeifa, Joseph G., Allen, Mary A., Hendrix, Josephina R., Read, Timothy, Rubin, Jonathan D., Dowell, Robin D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5848612/
https://www.ncbi.nlm.nih.gov/pubmed/29449408
http://dx.doi.org/10.1101/gr.225755.117
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author Azofeifa, Joseph G.
Allen, Mary A.
Hendrix, Josephina R.
Read, Timothy
Rubin, Jonathan D.
Dowell, Robin D.
author_facet Azofeifa, Joseph G.
Allen, Mary A.
Hendrix, Josephina R.
Read, Timothy
Rubin, Jonathan D.
Dowell, Robin D.
author_sort Azofeifa, Joseph G.
collection PubMed
description 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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spelling pubmed-58486122018-03-20 Enhancer RNA profiling predicts transcription factor activity Azofeifa, Joseph G. Allen, Mary A. Hendrix, Josephina R. Read, Timothy Rubin, Jonathan D. Dowell, Robin D. Genome Res Research 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. Cold Spring Harbor Laboratory Press 2018-03 /pmc/articles/PMC5848612/ /pubmed/29449408 http://dx.doi.org/10.1101/gr.225755.117 Text en © 2018 Azofeifa et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Research
Azofeifa, Joseph G.
Allen, Mary A.
Hendrix, Josephina R.
Read, Timothy
Rubin, Jonathan D.
Dowell, Robin D.
Enhancer RNA profiling predicts transcription factor activity
title Enhancer RNA profiling predicts transcription factor activity
title_full Enhancer RNA profiling predicts transcription factor activity
title_fullStr Enhancer RNA profiling predicts transcription factor activity
title_full_unstemmed Enhancer RNA profiling predicts transcription factor activity
title_short Enhancer RNA profiling predicts transcription factor activity
title_sort enhancer rna profiling predicts transcription factor activity
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5848612/
https://www.ncbi.nlm.nih.gov/pubmed/29449408
http://dx.doi.org/10.1101/gr.225755.117
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