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

Abstract

Despite much recent progress, our understanding of the principles of plant genome organization and its dynamics in three-dimensional space of interphase nuclei remains surprisingly limited. Notably, it is not clear how these processes could be affected by the size of a plant’s nuclear genome. In this study, DNA replication timing and interphase chromosome positioning were analyzed in seven Poaceae species that differ in their genome size. To provide a comprehensive picture, a suite of advanced, complementary methods was used: labeling of newly replicated DNA by EdU, isolation of nuclei at particular cell cycle phases by flow cytometric sorting, three-dimensional immuno-FISH, and confocal microscopy. Our results revealed conserved dynamics of DNA replication in all species, a similar replication timing order for telomeres and centromeres, as well as for euchromatin and heterochromatin regions, irrespective of genome size. Moreover, stable chromosome positioning was observed while transitioning through different stages of interphase. These findings expand upon earlier studies, in suggesting a more complex interplay exists between genome size, organization of repetitive DNA sequences along chromosomes, and higher order chromatin structure and its maintenance in interphase, albeit controlled by currently unknown factors.

Telomeres and Subtelomeres Dynamics in the Context of Early Chromosome Interactions During Meiosis and Their Implications in Plant Breeding

“…They suggest that sequences that are close together tend to replicate at the same time (Concia et al, 2018). A similar picture was found in a larger study involving time and position parameters of DNA replication in several Poaceae including wheat, oat, rye, barley, Brachypodium, rice, and maize (Němečková et al, 2020).…”

Analysis of the small chromosomal Prionium serratum (Cyperid) demonstrates the importance of reliable methods to differentiate between mono- and holocentricity

“…In general, different stages of the S phase are characterized by contrasting DNA replication patterns. The early S phase was characterized by dispersed EdU signals, and clustered EdU signals were typical for the late S phase (Costas et al 2011;Němečková et al 2020). Whether the replication behaviour of mono-and holocentric species differs is unkown yet.…”

A Multigraph model of the 3D genome

“…For instance, in plant nuclei, interphase chromosomes are organized in distinct territories 43,44 where landmark chromosomal regions have a well-defined orientation. A highly conserved aspect of chromatin organisation in large genome cereals, such as wheat and barley, is the orientation of their telomeres and centromeres into opposite poles of the nuclear periphery in a so-called "Rabl" configuration 45,46 . Rice nuclei in contrast, carrying the smallest genome among the grasses 47 , show "Rosette" configuration where pericentromeric repeat elements are located in the proximity of the nucleolus from which coding regions emerge as chromatin loops 46,48,49 .…”