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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2018
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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. |
format | Online Article Text |
id | pubmed-5848612 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
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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