Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq
Abstract
Understanding the mechanisms that regulate cell type-specific transcriptional programs requires developing a lexicon of their genomic regulatory elements. We developed a lineage-selective method to map transcriptional enhancers, regulatory genomic regions that activate transcription, in mice. Since most tissue-specific enhancers are bound by the transcriptional co-activator Ep300, we used Cre-directed, lineage-specific Ep300 biotinylation and pulldown on immobilized streptavidin followed by next generation sequencing of co-precipitated DNA to indentify lineage-specific enhancers. By driving this system with lineage-specific Cre transgenes, we mapped enhancers active in embryonic endothelial cells/blood or skeletal muscle. Analysis of these enhancers identified new transcription factor heterodimer motifs that likely regulate transcription in these lineages. Furthermore, we identified candidate enhancers that regulate adult heart- or lung- specific endothelial cell specialization. Our strategy for tissue-specific protein biotinylation opens new avenues for studying lineage-specific protein-DNA and protein-protein interactions.
Data availability
-
Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific p300 bioChIP-seqPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE88789).
-
Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICRPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE36027).
-
ChIP-seq from heart (ENCSR646GHA)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE82850).
-
ChIP-seq from heart (ENCSR123MLY)Publicly available at the NCBI Gene Expression Omnibus (accession no: GSM2191196).
-
ChIP-seq Accurately Predicts Tissue-Specific Activity of EnhancersPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE13845).
Article and author information
Author details
Funding
National Institutes of Health (U01HL098166; HL095712)
- William T Pu
American Heart Association (12EIA8440003)
- William T Pu
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: Animal experiments were performed under protocols approved by the Boston Children's Hospital Animal Care and Use Committee (protocols 13-08-2460R and 13-12-2601).
Copyright
© 2017, Zhou et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 5,446
- views
-
- 989
- downloads
-
- 58
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Citations by DOI
-
- 58
- citations for umbrella DOI https://doi.org/10.7554/eLife.22039