A flow cytometric method for estimating S-phase duration in plants

Blocking Deoxycytidine Kinase in Activated Lymphocytes Depletes Deoxycytidine Triphosphate Pools and Alters Cell Cycle Kinetics to Yield Less Disease in a Mouse Multiple Sclerosis Model

Autoreactive, aberrantly activated lymphocytes that target myelin antigens in the central nervous system (CNS) are primary drivers of the autoimmune disease multiple sclerosis (MS). Proliferating cells including activated lymphocytes require deoxyribonucleoside triphosphates (dNTPs) for DNA replication. dNTPs can be synthesised via the de novo pathway from precursors such as glucose and amino acids or the deoxyribonucleoside salvage pathway from extracellular deoxyribonucleosides. Deoxycytidine kinase (dCK) is the rate-limiting enzyme in the salvage pathway. In prior work, we showed that targeting dCK with the small molecule inhibitor TRE-515 limits clinical symptoms in two myelin oligodendrocyte glycoprotein (MOG)-induced experimental autoimmune encephalomyelitis (EAE) mouse models of MS and decreases the levels of activated CD4 T and B lymphocytes in vivo. However, whether targeting dCK limits disease in additional EAE models and how targeting dCK directly impacts activated and proliferating CD4 T and B cells has yet to be determined. Here, we show that dCK is activated in the lymph nodes and spleen in an EAE model induced by amino acids 139-151 of the proteolipid protein (PLP139-151) that is driven by CD4 T and B cells and is characterised by acute disease followed by disease remission. Treating this model with TRE-515 limits clinical symptoms and decreases the levels of activated CD4 T and B cells. In culture, CD4 T and B cells induce deoxyribonucleoside salvage following activation, and TRE-515 directly blocks CD4 T and B cell activation-induced proliferation and activation marker expression. TRE-515 decreases deoxycytidine triphosphate (dCTP) and deoxythymidine triphosphate (dTTP) pools and increases the length of time cells spend in S phase of the cell cycle without inducing a replication stress response in B cells. Our results suggest that dCK activity is required to supply needed dNTPs and to enable rapid cell division following lymphocyte activation against autoantigens in EAE mouse models.

Genome size, chromosome number variation and its correlation with stomatal characters for assessment of ploidy levels in a core subset of mulberry (Morus spp.) germplasm

The large size of the germplasm collection along with scanty information on their cytological and genome constitution have hindered well-planned breeding schemes in mulberry. To address the issue, a study was undertaken to investigate the variability in DNA content and genome size, chromosome number, ploidy and its relation with important stomatal characteristics among 162 mulberry germplasm. These germplasm comprise a core subset of 150 collections along with a representative collection of different mulberry species including the wild. Among the germplasm belonging to 16 species, we identified 122 diploids (2n = 28), 4 aneuploids (2n = 30), 13 triploids (2n = 42), 15 tetraploids (2n = 56), 7 hexaploids (2n = 84) and 1 dodecosaploid (2n = 308) based on the chromosome count. Most of the cultivated mulberries are found to be diploids. The mean nuclear 2C DNA content estimated by Flow cytometry, varied from 0.723±0.006 pg (M. australis, 2n = 2x) to 7.732 pg (M. nigra, 2n = 22x). The 2C DNA content positively correlated with the ploidy status and stomatal length (r = 0.814, p<0.001). Based on the 1Cx value, the study also suggests that the majority of the polyploid species have experienced genome downsizing in relation to their diploid progenitors. This study provides the most essential information on chromosome number, ploidy and DNA content to facilitate the utilization of a core subset of germplasm in the mulberry breeding program.

A simple pipeline for cell cycle kinetic studies in the root apical meristem

Root system architecture ultimately depends on precise signaling between different cells and tissues in the root apical meristem (RAM) and integration with environmental cues. This study describes a simple pipeline to simultaneously determine cellular parameters, nucleus geometry, and cell cycle kinetics in the RAM. The method uses marker-free techniques for nucleus and cell boundary detection, and 5-ethynyl-2'-deoxyuridine (EdU) staining for DNA replication quantification. Based on this approach, we characterized differences in cell volume, nucleus volume, and nucleus shape across different domains of the Arabidopsis RAM. We found that DNA replication patterns were cell layer and region dependent. G2 phase duration, which varied from 3.5 h in the pericycle to more than 4.5 h in the epidermis, was found to be associated with some features of nucleus geometry. Endocycle duration was determined as the time required to achieve 100% EdU-positive cells in the elongation zone and, as such, it was estimated to be in the region of 5 h for the epidermis and cortex. This experimental pipeline could be used to precisely map cell cycle duration in the RAM of mutants and in response to environmental stress in several plant species without the need for introgressing molecular cell cycle markers.

S Phase Duration Is Determined by Local Rate and Global Organization of Replication

The duration of the cell cycle has been extensively studied and a wide degree of variability exists between cells, tissues and organisms. However, the duration of S phase has often been neglected, due to the false assumption that S phase duration is relatively constant. In this paper, we describe the methodologies to measure S phase duration, summarize the existing knowledge about its variability and discuss the key factors that control it. The local rate of replication (LRR), which is a combination of fork rate (FR) and inter-origin distance (IOD), has a limited influence on S phase duration, partially due to the compensation between FR and IOD. On the other hand, the organization of the replication program, specifically the amount of replication domains that fire simultaneously and the degree of overlap between the firing of distinct replication timing domains, is the main determinant of S phase duration. We use these principles to explain the variation in S phase length in different tissues and conditions.

The Role of Topoisomerase II in DNA Repair and Recombination in Arabidopsis thaliana

DNA entanglements and supercoiling arise frequently during normal DNA metabolism. DNA topoisomerases are highly conserved enzymes that resolve the topological problems that these structures create. Topoisomerase II (TOPII) releases topological stress in DNA by removing DNA supercoils through breaking the two DNA strands, passing a DNA duplex through the break and religating the broken strands. TOPII performs key DNA metabolic roles essential for DNA replication, chromosome condensation, heterochromatin metabolism, telomere disentanglement, centromere decatenation, transmission of crossover (CO) interference, interlock resolution and chromosome segregation in several model organisms. In this study, we reveal the endogenous role of Arabidopsis thaliana TOPII in normal root growth and cell cycle, and mitotic DNA repair via homologous recombination. Additionally, we show that the protein is required for meiotic DSB repair progression, but not for CO formation. We propose that TOPII might promote mitotic HR DNA repair by relieving stress needed for HR strand invasion and D-loop formation.

Tools for Assessing Cell-Cycle Progression in Plants

Estimation of cell-cycle parameters is crucial for understanding the developmental programs established during the formation of an organism. A number of complementary approaches have been developed and adapted to plants to assess the cell-cycle status in different proliferative tissues. The most classical methods relying on metabolic labeling are still very much employed and give valuable information on cell-cycle progression in fixed tissues. However, the growing knowledge of plant cell-cycle regulators with defined expression pattern together with the development of fluorescent proteins technology enabled the generation of fusion proteins that function individually or in conjunction as cell-cycle reporters. Together with the improvement of imaging techniques, in vivo live imaging to monitor plant cell-cycle progression in normal growth conditions or in response to different stimuli has been possible. Here, we review these tools and their specific outputs for plant cell-cycle analysis.

Application-based guidelines for best practices in plant flow cytometry

Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.

Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf

BACKGROUND

The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely understood, which limits the value of transcriptome data to understand the process of chloroplast development.

RESULTS

Taking advantage of the developmental gradient in the bread wheat leaf, we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular compartment. This allows us to generate the first biologically-informed gene expression map of this leaf, with the entire developmental gradient from meristematic to fully differentiated cells captured. We show that the first phase of plastid development begins with organelle proliferation, which extends well beyond cell proliferation, and continues with the establishment and then the build-up of the plastid genetic machinery. The second phase is marked by the development of photosynthetic chloroplasts which occupy the available cellular space. Using a network reconstruction algorithm, we predict that known chloroplast gene expression regulators are differentially involved across those developmental stages.

CONCLUSIONS

Our analysis generates both the first wheat leaf transcriptional map and one of the most comprehensive descriptions to date of the developmental history of chloroplasts in higher plants. It reveals functionally distinct plastid and chloroplast development stages, identifies processes occurring in each of them, and highlights our very limited knowledge of the earliest drivers of plastid biogenesis, while providing a basis for their future identification.

In vitro and in vivo uterine metabolic disorders induced by silica nanoparticle through the AMPK signaling pathway

Exposure to silica nanoparticles (SiNPs) has been suggested to cause physical disorders, yet the effects of SiNPs on female reproduction have not been illustrated. This study was implemented to explore the reproductive toxicity of SiNPs on female and reveal its underlying mechanisms. Methodologically, the fluorescein isothiocyanate (FITC)-SiNPs were synthesized by coupling with FITC and then used to track the biodistribution of SiNPs in vitro and in vivo. In total, 30 mice were intratracheally injected 0.25 g of FITC-SiNPs, and 6 mice injected with the same volume of saline were used as controls. The results showed that SiNPs penetrated the cellular membrane, triggering apoptosis and inhibiting proliferation, tube formation, and invasion of trophoblast. Mechanistically, SiNPs was demonstrated to dysregulate Fbp2, Cpt1a, Scd1, and Pfkl, and further induced accumulation of pyruvate and fatty acid in mitochondria through the AMPK signaling pathway, which finally activated the Caspase-3-dependent apoptosis. Consistently, the similar alterations of these genes were detected in vivo, and the uterine inflammatory infiltration aggravated with the extension of the observation duration. These results suggested that SiNPs induced trophoblast apoptosis and uterine inflammation, and ultimately caused acute reproductive toxicity on female. The underlying mechanism might be explained by the dysregulation of Fbp2/Cpt1a/Pfkl/Scd1 axis, which promoted the overload of glucose and lipid through the AMPK signaling pathway. These findings were of great significance to guide a comprehensive understanding of the reproductive toxicity of SiNPs as well as the development of environmental standards.

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, whereas mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, whereas mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small interfering RNAs (siRNAs) and histone H3 lysine dimethylation (H3K9me2), without gaining CHH methylation. This suggests that spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation (RdDM) pathway. In contrast, loci that fail to produce siRNA may be targeted for demethylation when the cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.

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

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 ethynyl-2'-deoxyuridine, isolation of nuclei at particular cell cycle phases by flow cytometric sorting, three-dimensional immunofluorescence in situ hybridization, and confocal microscopy. Our results revealed conserved dynamics of DNA replication in all species, and 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 that 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.

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

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.

In traditional cell division, or mitosis, a cell’s genetic material is duplicated and then split between two daughter cells. In contrast, in some specialized cell types, the DNA is duplicated a second time without an intervening division step, resulting in cells that carry twice as much DNA. This phenomenon, which is called the endocycle, is common during plant development. At each step, DNA replication follows an ordered program in which highly compacted DNA is unraveled and replicated in sections at different times during the synthesis (S) phase. In plants, it is unclear whether traditional and endocycle programs are the same, especially since endocycling cells are typically in the process of differentiation. Using root tips of maize, we found that in comparison to replication in the mitotic cell cycle, there is a small portion of the genome whose replication in the endocycle is shifted in time, usually to later in S phase. Some of these regions are scattered around the genome and mostly coincide with active genes. However, the most prominent shifts occur in centromeres. The shift to later replication in centromeres is noteworthy because they orchestrate the process of separating duplicated chromosomes into daughter cells, a function that is not needed in the endocycle.

The genome size of clusterbean (Cyamopsis tetragonoloba) is significantly smaller compared to its wild relatives as estimated by flow cytometry

Clusterbean (C. tetragonoloba) is an important, leguminous vegetable and industrial crop with vast genetic diversity but meager genetic, cytological and genomic information. In the present study, an optimized procedure of flow cytometry was used to estimate the genome size of three clusterbean species, represented by C. tetragonoloba (cv. RGC-936) and two wild relatives (C. serreta and C. senegalensis). For accurate estimation of genomic content, singlet G₀/G₁ populations of multiple tissues such as leaves, hypocotyl, and matured seeds were determined and used along with three different plant species viz. Pisum sativum (as primary), Oryza sativa, and Glycine max (secondary), as external and internal reference standards. Seed tissue of the test sample and G. max provided the best estimate of nuclear DNA content in comparison to other sample tissues and reference standards. The genome size of C. tetragonoloba was detemined at 580.9±0.02Mbp (1C), while that of C. serreta and C. senegalensis was estimated at 979.6±0.02Mbp (1C) and 943.4±0.03Mbp (1C), respectively. Thus, the wild relatives harbor, nearly double the genome content of the cultivated cluster bean. Findings of this study will enrich genomic database of the legume family and can serve as the starting point for clusterbean evolutionary and genomics studies.

Re-activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing

Patterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.

Genome-Wide Analysis of the Arabidopsis Replication Timing Program

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 are 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, at high-resolution, the genome-wide replication timing program for Arabidopsis (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, noninteracting compartments. The temporal order of DNA replication within the early/mid compartment may be modulated largely by chromatin accessibility.

Replication of ribosomal DNA in Arabidopsis occurs both inside and outside the nucleolus during S phase progression

Ribosomal RNA genes (rDNA) have been used as valuable experimental systems in numerous studies. Here, we focus on elucidating the spatiotemporal organisation of rDNA replication in Arabidopsis thaliana To determine the subnuclear distribution of rDNA and the progression of its replication during the S phase, we apply 5-ethynyl-2'-deoxyuridine (EdU) labelling, fluorescence-activated cell sorting, fluorescence in situ hybridization and structured illumination microscopy. We show that rDNA is replicated inside and outside the nucleolus, where active transcription occurs at the same time. Nascent rDNA shows a maximum of nucleolar associations during early S phase. In addition to EdU patterns typical for early or late S phase, we describe two intermediate EdU profiles characteristic for mid S phase. Moreover, the use of lines containing mutations in the chromatin assembly factor-1 gene fas1 and wild-type progeny of fas1xfas2 crosses depleted of inactive copies allows for selective observation of the replication pattern of active rDNA. High-resolution data are presented, revealing the culmination of replication in the mid S phase in the nucleolus and its vicinity. Taken together, our results provide a detailed snapshot of replication of active and inactive rDNA during S phase progression.

Visualization of the Nucleolus Using Ethynyl Uridine

Thanks to recent innovative methodologies, key cellular processes such as replication or transcription can be visualized directly in situ in intact tissues. Many studies use so-called click iT chemistry where nascent DNA can be tracked by 5-ethynyl-2'-deoxyuridine (EdU), and nascent RNA by 5-ethynyl uridine (EU). While the labeling of replicating DNA by EdU has already been well established and further exploited in plants, the use of EU to reveal nascent RNA has not been developed to such an extent. In this article, we present a protocol for labeling of nucleolar RNA transcripts using EU and show that EU effectively highlights the nucleolus. The method is advantageous, because the need to prepare transgenic plants expressing fluorescently tagged nucleolar components when the nucleolus has to be visualized can be avoided.

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

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.