The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed
Brittany S. Sexton, Denis Avey, Brooke R. Druliner, Justin A. Fincher, Daniel L. Vera, Daniel J. Grau, Mark L. Borowsky, Shobhit Gupta, Senthil B. Girimurugan, Eric Chicken, Jinfeng Zhang, William S. Noble, Fanxiu Zhu, Robert E. Kingston, Jonathan H. Dennis
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.
https://doi.org/10.1101/gr.160150.113
10.1101/gr.160150.113
Dive into the research topics of 'The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed'. Together they form a unique fingerprint.
Nucleosomes Medicine & Life Sciences 100%
DNA Medicine & Life Sciences 47%
Human Herpesvirus 8 Medicine & Life Sciences 29%
Chromatin Medicine & Life Sciences 13%
Computer Simulation Medicine & Life Sciences 7%
Mammals Medicine & Life Sciences 6%
Genes Medicine & Life Sciences 6%
Sexton, B. S., Avey, D., Druliner, B. R., Fincher, J. A., Vera, D. L., Grau, D. J., Borowsky, M. L., Gupta, S., Girimurugan, S. B., Chicken, E., Zhang, J., Noble, W. S., Zhu, F., Kingston, R. E., & Dennis, J. H. (2014). The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed. Genome Research, 24(2), 251-259. https://doi.org/10.1101/gr.160150.113
The spring-loaded genome : Nucleosome redistributions are widespread, transient, and DNA-directed. / Sexton, Brittany S.; Avey, Denis; Druliner, Brooke R.; Fincher, Justin A.; Vera, Daniel L.; Grau, Daniel J.; Borowsky, Mark L.; Gupta, Shobhit; Girimurugan, Senthil B.; Chicken, Eric; Zhang, Jinfeng; Noble, William S.; Zhu, Fanxiu; Kingston, Robert E.; Dennis, Jonathan H.
In: Genome Research, Vol. 24, No. 2, 02.2014, p. 251-259.
Sexton, BS, Avey, D, Druliner, BR, Fincher, JA, Vera, DL, Grau, DJ, Borowsky, ML, Gupta, S, Girimurugan, SB, Chicken, E, Zhang, J, Noble, WS, Zhu, F, Kingston, RE & Dennis, JH 2014, 'The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed', Genome Research, vol. 24, no. 2, pp. 251-259. https://doi.org/10.1101/gr.160150.113
Sexton BS, Avey D, Druliner BR, Fincher JA, Vera DL, Grau DJ et al. The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed. Genome Research. 2014 Feb;24(2):251-259. https://doi.org/10.1101/gr.160150.113
Sexton, Brittany S. ; Avey, Denis ; Druliner, Brooke R. ; Fincher, Justin A. ; Vera, Daniel L. ; Grau, Daniel J. ; Borowsky, Mark L. ; Gupta, Shobhit ; Girimurugan, Senthil B. ; Chicken, Eric ; Zhang, Jinfeng ; Noble, William S. ; Zhu, Fanxiu ; Kingston, Robert E. ; Dennis, Jonathan H. / The spring-loaded genome : Nucleosome redistributions are widespread, transient, and DNA-directed. In: Genome Research. 2014 ; Vol. 24, No. 2. pp. 251-259.
@article{39fd19c05df54433b6cde9a039687d5e,
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.",
author = "Sexton, {Brittany S.} and Denis Avey and Druliner, {Brooke R.} and Fincher, {Justin A.} and Vera, {Daniel L.} and Grau, {Daniel J.} and Borowsky, {Mark L.} and Shobhit Gupta and Girimurugan, {Senthil B.} and Eric Chicken and Jinfeng Zhang and Noble, {William S.} and Fanxiu Zhu and Kingston, {Robert E.} and Dennis, {Jonathan H.}",
doi = "10.1101/gr.160150.113",
journal = "Genome Research",
publisher = "Cold Spring Harbor Laboratory Press",
T1 - The spring-loaded genome
T2 - Nucleosome redistributions are widespread, transient, and DNA-directed
AU - Sexton, Brittany S.
AU - Avey, Denis
AU - Druliner, Brooke R.
AU - Fincher, Justin A.
AU - Vera, Daniel L.
AU - Grau, Daniel J.
AU - Borowsky, Mark L.
AU - Gupta, Shobhit
AU - Girimurugan, Senthil B.
AU - Chicken, Eric
AU - Zhang, Jinfeng
AU - Noble, William S.
AU - Zhu, Fanxiu
AU - Kingston, Robert E.
AU - Dennis, Jonathan H.
N2 - 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.
AB - 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.
U2 - 10.1101/gr.160150.113
DO - 10.1101/gr.160150.113
JO - Genome Research
JF - Genome Research