ArticlePLoS genetics2010
Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state.
Article in PLoS genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed, 77 citations in OpenAlex.
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing.The Plant journal : for cell and molecular biology · 2025Article
- An Arabidopsis Cell Culture With Weak Circadian Rhythms Under Constant Light Compared With Constant Dark Can Be Rescued by ELF3.Plant direct · 2024Article
- A Protocol for Genome-Wide Analysis of DNA Replication Timing in Intact Root Tips.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The 3D Genome: From Structure to Function.International journal of molecular sciences · 2021Review
- Hydroxyurea and Caffeine Impact pRb-like Protein-Dependent Chromatin Architecture Profiles in Interphase Cells ofInternational journal of molecular sciences · 2021Article
- TheProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation.Current biology : CB · 2021Article
- Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin.Plant physiology · 2020Article
- Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing.Scientific reports · 2018Article
- Genome-Wide Analysis of the Arabidopsis Replication Timing Program.Plant physiology · 2018Article
- Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress.BMC plant biology · 2017Article
- Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis.PLoS genetics · 2017Article
- Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (The Plant cell · 2017Article
- Repliscan: a tool for classifying replication timing regions.BMC bioinformatics · 2017Article
- Take a look at plant DNA replication: Recent insights and new questions.Plant signaling & behavior · 2017Article
- Genetic and epigenetic variation of transposable elements in Arabidopsis.Current opinion in plant biology · 2017Review
- Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- A flow cytometric method for estimating S-phase duration in plants.Journal of experimental botany · 2016Article
- Abundant protein phosphorylation potentially regulates Arabidopsis anther development.Journal of experimental botany · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 4 institutions in 2 countries.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.