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Elife. 2017 Jan 25;6. pii: e22039. doi: 10.7554/eLife.22039.

Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq.

Author information

1
Department of Cardiology, Boston Children's Hospital, Boston, United States.
2
Department of Biochemistry, Institute of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
3
Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
4
State Key Laboratory of Cell Biology, CAS center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
5
Harvard Stem Cell Institute, Harvard University, Cambridge, United States.
#
Contributed equally

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 identify 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.

KEYWORDS:

angiogenesis; chromosomes; developmental biology; endothelial cell; genes; mouse; p300; stem cells; transcriptional enhancer

PMID:
28121289
PMCID:
PMC5295818
DOI:
10.7554/eLife.22039
[Indexed for MEDLINE]
Free PMC Article

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