title: SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers.
abstract: We developed Split DamID (SpDamID), a protein complementation version of DamID, to mark genomic DNA bound in vivo by interacting or juxtapositioned transcription factors. Inactive halves of DAM (DNA adenine methyltransferase) were fused to protein pairs to be queried. Either direct interaction between proteins or proximity enabled DAM reconstitution and methylation of adenine in GATC. Inducible SpDamID was used to analyze Notch-mediated transcriptional activation. We demonstrate that Notch complexes label RBP sites broadly across the genome and show that a subset of these complexes that recruit MAML and p300 undergo changes in chromatin accessibility in response to Notch signaling. SpDamID differentiates between monomeric and dimeric binding, thereby allowing for identification of half-site motifs used by Notch dimers. Motif enrichment of Notch enhancers coupled with SpDamID reveals co-targeting of regulatory sequences by Notch and Runx1. SpDamID represents a sensitive and powerful tool that enables dynamic analysis of combinatorial protein-DNA transactions at a genome-wide level.
authors.affiliation: Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA. Electronic address: matthew.hass@cchmc.org.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Hass
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, MO 63108, USA.
authors.forename: Hien-Haw
authors.initials: HH
authors.lastname: Liow
authors.affiliation: School of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH 45221, USA; Center for Autoimmune Genomics and Etiology (CAGE) and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Xiaoting
authors.initials: X
authors.lastname: Chen
authors.affiliation: Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Ankur
authors.initials: A
authors.lastname: Sharma
authors.affiliation: Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan.
authors.forename: Yukiko U
authors.initials: YU
authors.lastname: Inoue
authors.affiliation: Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan.
authors.forename: Takayoshi
authors.initials: T
authors.lastname: Inoue
authors.affiliation: Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA.
authors.forename: Ashley
authors.initials: A
authors.lastname: Reeb
authors.affiliation: Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Martens
authors.affiliation: Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA.
authors.forename: Mary
authors.initials: M
authors.lastname: Fulbright
authors.affiliation: Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA.
authors.forename: Saravanan
authors.initials: S
authors.lastname: Raju
authors.affiliation: Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Stevens
authors.affiliation: Department of Developmental Biology, Washington University, Saint Louis, MO 63110, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Boyle
authors.affiliation: Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Pediatric Urology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Joo-Seop
authors.initials: JS
authors.lastname: Park
authors.affiliation: Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Autoimmune Genomics and Etiology (CAGE) and Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Weirauch
authors.affiliation: Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, MO 63108, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Brent
authors.affiliation: Division of Developmental Biology, Children's Hospital Medical Center, Cincinnati, OH 45229, USA. Electronic address: raphael.kopan@cchmc.org.
authors.forename: Raphael
authors.initials: R
authors.lastname: Kopan
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002460:Cell Line; D004247:DNA / Q000235:genetics* / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D008822:Mice, Transgenic; D015336:Molecular Probe Techniques; D008969:Molecular Sequence Data; D011485:Protein Binding; D051880:Receptors, Notch / Q000502:physiology*
chemical_list: D051880:Receptors, Notch; D004247:DNA