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

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

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Biotinylation
  • Chromatin Immunoprecipitation / methods
  • E1A-Associated p300 Protein / metabolism*
  • Enhancer Elements, Genetic*
  • Mice
  • Protein Processing, Post-Translational
  • Sequence Analysis, DNA
  • Transcription Factors*
  • Transcription, Genetic*

Substances

  • Transcription Factors
  • E1A-Associated p300 Protein
  • Ep300 protein, mouse