Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Abstract

All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ;32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.

DNA replication and chromosome positioning throughout the interphase in three dimensional space of plant nuclei

“…In middle S phase, replication was almost evenly dispersed along the entire chromosomes and only slightly increased in the interstitial regions of chromosome arms. These findings confirmed the recent results made in Arabidopsis and maize obtained by Repli-seq analysis and corresponded to the gene density of their chromosome profiles (Wear et al , 2017, Zynda et al , 2017; Concia et al , 2018). Kwasniewska et al (2018) showed that terminal parts of barley chromosomes replicated in early S phase, whole chromosomes were covered with EdU signal at middle S phase and centromeric parts of chromosomes were replicated in late S phase.…”

Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin

“…As a consequence, it is not known if the conclusions from these experiments accurately describe DNA replication under normal conditions. To address this concern, we developed a new functional assay by combining brief labeling with 5-ethynyl-2'-deoxy-uridine (EdU) (Bass et al, 2015;Ramachandran and Henikoff, 2016;Dvořáčková et al, 2018;Macheret and Halazonetis, 2018;Tubbs et al, 2018;Macheret and Halazonetis, 2019) with flow sorting (Wear et al, 2016;Wear et al, 2017;Concia et al, 2018) to isolate nuclei in which replication has just begun, so that label is incorporated close to the points of initiation. This was followed by immunoprecipitation and characterization of the labeled DNA.…”

Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize

“…2f). DNA replication initiation regions (Wear et al 2017) were associated with both group A and group B pan-And-CNSs (Fig. 2g).…”

“…The DNA duplication signals files were downloaded from the original publication (Wear et al 2017). And the maize reference V3 coordinates were uplifted to V4 coordinates using CrossMap v0.2.8 (Zhao et al 2014) and the chain file released from ensembl website.…”