Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots


Autoři: Emily E. Wear aff001;  Jawon Song aff002;  Gregory J. Zynda aff002;  Leigh Mickelson-Young aff001;  Chantal LeBlanc aff003;  Tae-Jin Lee aff001;  David O. Deppong aff001;  George C. Allen aff004;  Robert A. Martienssen aff003;  Matthew W. Vaughn aff002;  Linda Hanley-Bowdoin aff001;  William F. Thompson aff001
Působiště autorů: Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America aff001;  Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America aff002;  Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America aff003;  Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America aff004
Vyšlo v časopise: Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots. PLoS Genet 16(10): e32767. doi:10.1371/journal.pgen.1008623
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008623

Souhrn

Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed.

Klíčová slova:

Cell cycle and cell division – Centromeres – DNA replication – Gene expression – Genomic signal processing – Maize – Plant genomics – Synthesis phase


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