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Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork.

Publication ,  Journal Article
Gutiérrez, MP; MacAlpine, HK; MacAlpine, DM
Published in: Genome Res
July 2019

Proper regulation and maintenance of the epigenome is necessary to preserve genome function. However, in every cell division, the epigenetic state is disassembled and then reassembled in the wake of the DNA replication fork. Chromatin restoration on nascent DNA is a complex and regulated process that includes nucleosome assembly and remodeling, deposition of histone variants, and the re-establishment of transcription factor binding. To study the genome-wide dynamics of chromatin restoration behind the DNA replication fork, we developed nascent chromatin occupancy profiles (NCOPs) to comprehensively profile nascent and mature chromatin at nucleotide resolution. Although nascent chromatin is inherently less organized than mature chromatin, we identified locus-specific differences in the kinetics of chromatin maturation that were predicted by the epigenetic landscape, including the histone variant H2AZ, which marked loci with rapid maturation kinetics. The chromatin maturation at origins of DNA replication was dependent on whether the origin underwent initiation or was passively replicated from distal-originating replication forks, suggesting distinct chromatin assembly mechanisms surrounding activated and disassembled prereplicative complexes. Finally, we identified sites that were only occupied transiently by DNA-binding factors following passage of the replication fork, which may provide a mechanism for perturbations of the DNA replication program to shape the regulatory landscape of the genome.

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

July 2019

Volume

29

Issue

7

Start / End Page

1123 / 1133

Location

United States

Related Subject Headings

  • Saccharomyces cerevisiae
  • Replication Origin
  • Nucleosomes
  • Histones
  • DNA-Binding Proteins
  • DNA, Bacterial
  • DNA Replication
  • Chromosome Mapping
  • Chromatin Assembly and Disassembly
  • Chromatin
 

Citation

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Gutiérrez, M. P., MacAlpine, H. K., & MacAlpine, D. M. (2019). Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork. Genome Res, 29(7), 1123–1133. https://doi.org/10.1101/gr.243386.118
Gutiérrez, Mónica P., Heather K. MacAlpine, and David M. MacAlpine. “Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork.Genome Res 29, no. 7 (July 2019): 1123–33. https://doi.org/10.1101/gr.243386.118.
Gutiérrez, Mónica P., et al. “Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork.Genome Res, vol. 29, no. 7, July 2019, pp. 1123–33. Pubmed, doi:10.1101/gr.243386.118.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

July 2019

Volume

29

Issue

7

Start / End Page

1123 / 1133

Location

United States

Related Subject Headings

  • Saccharomyces cerevisiae
  • Replication Origin
  • Nucleosomes
  • Histones
  • DNA-Binding Proteins
  • DNA, Bacterial
  • DNA Replication
  • Chromosome Mapping
  • Chromatin Assembly and Disassembly
  • Chromatin