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Arabidopsis DNA replication initiates in intergenic, AT-rich open chromatin.

Authors
  • Wheeler, Emily1
  • Brooks, Ashley M2
  • Concia, Lorenzo3
  • Vera, Daniel4
  • Wear, Emily Elizabeth5
  • LeBlanc, Chantal6
  • Ramu, Umamaheswari7
  • Vaughn, Matthew W8
  • Bass, Hank9
  • Martienssen, Robert10
  • Thompson, William F11
  • Hanley-Bowdoin, Linda12
  • 1 North Carolina State University CITY: Raleigh STATE: NC United States Of America [US] [email protected] , (United States)
  • 2 North Carolina State University CITY: Raleigh STATE: North Carolina United States Of America [US]. , (United States)
  • 3 École normale supérieure CITY: Paris POSTAL_CODE: 75005 France [FR]. , (France)
  • 4 Florida State University CITY: Tallahassee POSTAL_CODE: 32306 United States Of America [US]. , (United States)
  • 5 North Carolina State University CITY: Raleigh STATE: NC POSTAL_CODE: 27606 United States Of America [US]. , (United States)
  • 6 Yale University CITY: New Haven STATE: CT United States Of America [US]. , (United States)
  • 7 Cold Spring Harbor Laboratory CITY: Cold Spring Harbor STATE: NY United States Of America [US]. , (United States)
  • 8 University of Texas at Austin 10100 Burnet Rd, Bldg 196, Ste 1.101 CITY: Austin STATE: Texas POSTAL_CODE: 78758 United States Of America [US]. , (United States)
  • 9 Florida State University CITY: Tallahassee STATE: Florida POSTAL_CODE: 32306-4370 United States Of America [US]. , (United States)
  • 10 Cold Spring Harbor CITY: Cold Spring Harbor STATE: New York POSTAL_CODE: 11724 United States Of America [US]. , (United States)
  • 11 North Carolina State University CITY: Raleigh STATE: North Carolina POSTAL_CODE: 27695 United States Of America [US]. , (United States)
  • 12 North Carolina State University CITY: Raleigh STATE: North Carolina POSTAL_CODE: 27695-7622 United States Of America [US]. , (United States)
Type
Published Article
Journal
Plant physiology
Publication Date
Mar 23, 2020
Identifiers
DOI: 10.1104/pp.19.01520
PMID: 32205451
Source
Medline
Language
English
License
Unknown

Abstract

The selection and firing of DNA replication origins play key roles in ensuring that eukaryotes accurately replicate their genomes. This process is not well documented in plants due in large measure to difficulties in working with plant systems. We developed a new functional assay to label and map very early replicating loci that must, by definition, include at least a subset of replication origins. Arabidopsis thaliana cells were briefly labeled with 5-ethynyl-2'-deoxy-uridine, and nuclei were subjected to two-parameter flow sorting. We identified more than 5500 loci as initiation regions (IRs), the first regions to replicate in very early S phase. These were classified as strong or weak IRs based on the strength of their replication signals. Strong initiation regions were evenly spaced along chromosomal arms and depleted in centromeres, while weak initiation regions were enriched in centromeric regions. IRs are AT-rich sequences flanked by more GC-rich regions and located predominantly in intergenic regions. Nuclease sensitivity assays indicated that IRs are associated with accessible chromatin. Based on these observations, initiation of plant DNA replication shows some similarity to, but is also distinct from, initiation in other well-studied eukaryotic systems. {copyright, serif} 2020 American Society of Plant Biologists. All rights reserved.

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