Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state

Lee, Tae-Jin, Pascuzzi, Pete E., Settlage, Sharon B., Shultz, Randall W., Tanurdzic, Milos, Rabinowicz, Pablo D., Menges, Margit, Zheng, Ping, Main, Dorrie, Murray, James A. H., Sosinski, Bryon, Allen, George C., Martienssen, Robert A., Hanley-Bowdoin, Linda, Vaughn, Matthew W. and Thompson, William F. (2010) Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PLoS Genetics, 6 6: e1000982.1-e1000982.18. doi:10.1371/journal.pgen.1000982


Author Lee, Tae-Jin
Pascuzzi, Pete E.
Settlage, Sharon B.
Shultz, Randall W.
Tanurdzic, Milos
Rabinowicz, Pablo D.
Menges, Margit
Zheng, Ping
Main, Dorrie
Murray, James A. H.
Sosinski, Bryon
Allen, George C.
Martienssen, Robert A.
Hanley-Bowdoin, Linda
Vaughn, Matthew W.
Thompson, William F.
Title Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state
Journal name PLoS Genetics   Check publisher's open access policy
ISSN 1553-7390
1553-7404
Publication date 2010-06
Sub-type Article (original research)
DOI 10.1371/journal.pgen.1000982
Open Access Status DOI
Volume 6
Issue 6
Start page e1000982.1
End page e1000982.18
Total pages 18
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Language eng
Formatted abstract
DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4) during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac) was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated with initiation zones and replication origins.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article # e1000982

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Biological Sciences Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 36 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 43 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Mon, 08 Apr 2013, 22:04:08 EST by Gail Walter on behalf of School of Biological Sciences