title: Interdomain Communication of the Chd1 Chromatin Remodeler across the DNA Gyres of the Nucleosome.
abstract: Chromatin remodelers use a helicase-like ATPase motor to reposition and reorganize nucleosomes along genomic DNA. Yet, how the ATPase motor communicates with other remodeler domains in the context of the nucleosome has so far been elusive. Here, we report for the Chd1 remodeler a unique organization of domains on the nucleosome that reveals direct domain-domain communication. Site-specific cross-linking shows that the chromodomains and ATPase motor bind to adjacent SHL1 and SHL2 sites, respectively, on nucleosomal DNA and pack against the DNA-binding domain on DNA exiting the nucleosome. This domain arrangement spans the two DNA gyres of the nucleosome and bridges both ends of a wrapped, ∼90-bp nucleosomal loop of DNA, suggesting a means for nucleosome assembly. This architecture illustrates how Chd1 senses DNA outside the nucleosome core and provides a basis for nucleosome spacing and directional sliding away from transcription factor barriers.
authors.affiliation: T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA.
authors.forename: Ilana M
authors.initials: IM
authors.lastname: Nodelman
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Franziska
authors.initials: F
authors.lastname: Bleichert
authors.affiliation: T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA.
authors.forename: Ashok
authors.initials: A
authors.lastname: Patel
authors.affiliation: T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA.
authors.forename: Ren
authors.initials: R
authors.lastname: Ren
authors.affiliation: T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA.
authors.forename: Kyle C
authors.initials: KC
authors.lastname: Horvath
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Berger
authors.affiliation: T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Electronic address: gdbowman@jhu.edu.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Bowman
mesh_terms: D000818:Animals; D042002:Chromatin Assembly and Disassembly; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D009707:Nucleosomes / Q000235:genetics; D011485:Protein Binding; D000072417:Protein Domains; D014982:Xenopus laevis
chemical_list: D004268:DNA-Binding Proteins; D009707:Nucleosomes; D004247:DNA
keywords: CHD remodeler; DNA unwrapping; ISWI remodeler; SF2 ATPase; SHL2; chromatin remodeling; chromodomains; nucleosome assembly; nucleosome sliding; superhelical location 2