title: The spring-loaded genome: nucleosome redistributions are widespread, transient, and DNA-directed.
abstract: Nucleosome occupancy plays a key role in regulating access to eukaryotic genomes. Although various chromatin regulatory complexes are known to regulate nucleosome occupancy, the role of DNA sequence in this regulation remains unclear, particularly in mammals. To address this problem, we measured nucleosome distribution at high temporal resolution in human cells at hundreds of genes during the reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV). We show that nucleosome redistribution peaks at 24 h post-KSHV reactivation and that the nucleosomal redistributions are widespread and transient. To clarify the role of DNA sequence in these nucleosomal redistributions, we compared the genes with altered nucleosome distribution to a sequence-based computer model and in vitro-assembled nucleosomes. We demonstrate that both the predicted model and the assembled nucleosome distributions are concordant with the majority of nucleosome redistributions at 24 h post-KSHV reactivation. We suggest a model in which loci are held in an unfavorable chromatin architecture and "spring" to a transient intermediate state directed by DNA sequence information. We propose that DNA sequence plays a more considerable role in the regulation of nucleosome positions than was previously appreciated. The surprising findings that nucleosome redistributions are widespread, transient, and DNA-directed shift the current perspective regarding regulation of nucleosome distribution in humans.
authors: Department of Biological Science, The Florida State University, Tallahassee, Florida 32306-4295, USA;
authors: Brittany S
authors: BS
authors: Sexton
authors: Denis
authors: D
authors: Avey
authors: Brooke R
authors: BR
authors: Druliner
authors: Justin A
authors: JA
authors: Fincher
authors: Daniel L
authors: DL
authors: Vera
authors: Daniel J
authors: DJ
authors: Grau
authors: Mark L
authors: ML
authors: Borowsky
authors: Shobhit
authors: S
authors: Gupta
authors: Senthil B
authors: SB
authors: Girimurugan
authors: Eric
authors: E
authors: Chicken
authors: Jinfeng
authors: J
authors: Zhang
authors: William S
authors: WS
authors: Noble
authors: Fanxiu
authors: F
authors: Zhu
authors: Robert E
authors: RE
authors: Kingston
authors: Jonathan H
authors: JH
authors: Dennis
mesh_terms: D002843:Chromatin / Q000235:genetics*; D003198:Computer Simulation; D015894:Genome, Human; D019288:Herpesvirus 8, Human / Q000235:genetics*; D006801:Humans; D008957:Models, Genetic; D009707:Nucleosomes / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014775:Virus Activation / Q000235:genetics*
chemical_list: D002843:Chromatin; D009707:Nucleosomes