Genome-Wide Analysis of the Arabidopsis thaliana Replication Timing Program

Concia, L., Brooks, A. M., Wheeler, E., Zynda, G., Wear, E. E., LeBlanc, C., Song, J., Lee, T. J., Pascuzzi, P. E., Martienssen, R., Vaughn, M. W., Thompson, W., Hanley-Bowdoin, L. (January 2018) Genome-Wide Analysis of the Arabidopsis thaliana Replication Timing Program. Plant Physiol. ISSN 0032-0889

DOI: 10.1104/pp.17.01537


Eukaryotes use a temporally regulated process, known as the replication timing program, to ensure that their genomes are fully and accurately duplicated during S phase. Replication timing programs are predictive of genomic features and activity, and considered to be functional readouts of chromatin organization. Although replication timing programs have been described for yeast and animal systems, much less is known about the temporal regulation of plant DNA replication or its relationship to genome sequence and chromatin structure. We used the thymidine analog, 5-ethynyl-2'-deoxyuridine, in combination with flow sorting and Repli-Seq to describe a high-resolution, genome-wide replication timing program for Arabidopsis thaliana Col-0 suspension cells. We identified genomic regions that replicate predominantly during early, mid and late S phase, and correlated these regions with genomic features and with data for chromatin state, accessibility and long-distance interaction. Arabidopsis chromosome arms tend to replicate early while pericentromeric regions replicate late. Early and mid-replicating regions are gene-rich and predominantly euchromatic, while late regions are rich in transposable elements and primarily heterochromatic. However, the distribution of chromatin states across the different times is complex, with each replication time corresponding to a mixture of states. Early and mid-replicating sequences interact with each other and not with late sequences, but early regions are more accessible than mid regions. The replication timing program in Arabidopsis reflects a bipartite genomic organization with early/mid replicating regions and late regions forming separate, non-interacting compartments. The temporal order of DNA replication within the early/mid compartment may be modulated largely by chromatin accessibility.

Item Type: Paper
Subjects: organism description > plant > Arabidopsis
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Martienssen lab
Depositing User: Matt Covey
Date: 4 January 2018
Date Deposited: 10 Jan 2018 20:02
Last Modified: 05 Apr 2018 16:18
PMCID: PMC5841712
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