title: 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 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.
authors.affiliation: Department of Cardiology, Boston Children's Hospital, Boston, United States.
authors.forename: Pingzhu
authors.initials: P
authors.lastname: Zhou
authors.affiliation: Department of Cardiology, Boston Children's Hospital, Boston, United States.
authors.forename: Fei
authors.initials: F
authors.lastname: Gu
authors.affiliation: Department of Biochemistry, Institute of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
authors.forename: Lina
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Cardiology, Boston Children's Hospital, Boston, United States.
authors.forename: Brynn N
authors.identifier: 0000-0001-6470-6588
authors.initials: BN
authors.lastname: Akerberg
authors.affiliation: Department of Cardiology, Boston Children's Hospital, Boston, United States.
authors.forename: Qing
authors.initials: Q
authors.lastname: Ma
authors.affiliation: Department of Cardiology, Boston Children's Hospital, Boston, United States.
authors.forename: Kai
authors.initials: K
authors.lastname: Li
authors.affiliation: Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
authors.forename: Aibin
authors.identifier: 0000-0002-3489-2305
authors.initials: A
authors.lastname: He
authors.affiliation: Department of Cardiology, Boston Children's Hospital, Boston, United States.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Lin
authors.affiliation: Department of Cardiology, Boston Children's Hospital, Boston, United States.
authors.forename: Sean M
authors.initials: SM
authors.lastname: Stevens
authors.affiliation: 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.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhou
authors.affiliation: Department of Cardiology, Boston Children's Hospital, Boston, United States.|Harvard Stem Cell Institute, Harvard University, Cambridge, United States.
authors.forename: William T
authors.identifier: 0000-0002-4551-8079
authors.initials: WT
authors.lastname: Pu
mesh_terms: D000818:Animals; D019921:Biotinylation; D047369:Chromatin Immunoprecipitation / Q000379:methods; D050881:E1A-Associated p300 Protein / Q000378:metabolism*; D004742:Enhancer Elements, Genetic; D051379:Mice; D011499:Protein Processing, Post-Translational; D017422:Sequence Analysis, DNA; D014157:Transcription Factors; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors; D050881:E1A-Associated p300 Protein; C494361:Ep300 protein, mouse
keywords: angiogenesis; chromosomes; developmental biology; endothelial cell; genes; mouse; p300; stem cells; transcriptional enhancer