Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state.
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 u...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2010-06-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC2883604?pdf=render |
| _version_ | 1828340322785034240 |
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| author | Tae-Jin Lee Pete E Pascuzzi Sharon B Settlage Randall W Shultz Milos Tanurdzic Pablo D Rabinowicz Margit Menges Ping Zheng Dorrie Main James A H Murray Bryon Sosinski George C Allen Robert A Martienssen Linda Hanley-Bowdoin Matthew W Vaughn William F Thompson |
| author_facet | Tae-Jin Lee Pete E Pascuzzi Sharon B Settlage Randall W Shultz Milos Tanurdzic Pablo D Rabinowicz Margit Menges Ping Zheng Dorrie Main James A H Murray Bryon Sosinski George C Allen Robert A Martienssen Linda Hanley-Bowdoin Matthew W Vaughn William F Thompson |
| author_sort | Tae-Jin Lee |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T22:54:03Z |
| format | Article |
| id | doaj.art-81f85c00f18f4ebbbab5f78ac9993280 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-13T22:54:03Z |
| publishDate | 2010-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-81f85c00f18f4ebbbab5f78ac99932802022-12-22T02:26:04ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042010-06-0166e100098210.1371/journal.pgen.1000982Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state.Tae-Jin LeePete E PascuzziSharon B SettlageRandall W ShultzMilos TanurdzicPablo D RabinowiczMargit MengesPing ZhengDorrie MainJames A H MurrayBryon SosinskiGeorge C AllenRobert A MartienssenLinda Hanley-BowdoinMatthew W VaughnWilliam F ThompsonDNA 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.http://europepmc.org/articles/PMC2883604?pdf=render |
| spellingShingle | Tae-Jin Lee Pete E Pascuzzi Sharon B Settlage Randall W Shultz Milos Tanurdzic Pablo D Rabinowicz Margit Menges Ping Zheng Dorrie Main James A H Murray Bryon Sosinski George C Allen Robert A Martienssen Linda Hanley-Bowdoin Matthew W Vaughn William F Thompson Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PLoS Genetics |
| title | Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. |
| title_full | Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. |
| title_fullStr | Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. |
| title_full_unstemmed | Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. |
| title_short | Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. |
| title_sort | arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state |
| url | http://europepmc.org/articles/PMC2883604?pdf=render |
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