The synchronization manifesto: a critique of whole‐culture synchronization

Transcription-replication interactions reveal bacterial genome regulation

Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome1. In bacteria, the relationship between the regulatory architecture of a gene and its expression is well understood for individual model gene circuits2,3. However, a broader perspective of these dynamics at the genome scale is lacking, in part because bacterial transcriptomics has hitherto captured only a static snapshot of expression averaged across millions of cells4. As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on the transcriptional response of each gene to its own replication, which we term the transcription-replication interaction profile (TRIP). Analysing single-bacterium RNA-sequencing data, we found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal the local regulatory context of a gene. Whereas the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, and this is shaped by factors such as intra-operon position and repression state. By revealing the underlying mechanistic drivers of gene expression heterogeneity, this work provides a quantitative, biophysical framework for modelling replication-dependent expression dynamics.

A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation

Cell cycle transitions result from global changes in protein phosphorylation states triggered by cyclin-dependent kinases (CDKs). To understand how this complexity produces an ordered and rapid cellular reorganisation, we generated a high-resolution map of changing phosphosites throughout unperturbed early cell cycles in single Xenopus embryos, derived the emergent principles through systems biology analysis, and tested them by biophysical modelling and biochemical experiments. We found that most dynamic phosphosites share two key characteristics: they occur on highly disordered proteins that localise to membraneless organelles, and are CDK targets. Furthermore, CDK-mediated multisite phosphorylation can switch homotypic interactions of such proteins between favourable and inhibitory modes for biomolecular condensate formation. These results provide insight into the molecular mechanisms and kinetics of mitotic cellular reorganisation.

Increasing the throughput of sensitive proteomics by plexDIA

Current mass spectrometry methods enable high-throughput proteomics of large sample amounts, but proteomics of low sample amounts remains limited in depth and throughput. To increase the throughput of sensitive proteomics, we developed an experimental and computational framework, called plexDIA, for simultaneously multiplexing the analysis of peptides and samples. Multiplexed analysis with plexDIA increases throughput multiplicatively with the number of labels without reducing proteome coverage or quantitative accuracy. By using three-plex non-isobaric mass tags, plexDIA enables quantification of threefold more protein ratios among nanogram-level samples. Using 1-hour active gradients, plexDIA quantified ~8,000 proteins in each sample of labeled three-plex sets and increased data completeness, reducing missing data more than twofold across samples. Applied to single human cells, plexDIA quantified ~1,000 proteins per cell and achieved 98% data completeness within a plexDIA set while using ~5 minutes of active chromatography per cell. These results establish a general framework for increasing the throughput of sensitive and quantitative protein analysis.

Exploring functional protein covariation across single cells using nPOP

BACKGROUND

Many biological processes, such as cell division cycle and drug resistance, are reflected in protein covariation across single cells. This covariation can be quantified and interpreted by single-cell mass spectrometry with sufficiently high throughput and accuracy.

RESULTS

Here, we describe nPOP, a method that enables simultaneous sample preparation of thousands of single cells, including lysing, digesting, and labeling individual cells in volumes of 8-20 nl. nPOP uses piezo acoustic dispensing to isolate individual cells in 300 pl volumes and performs all subsequent sample preparation steps in small droplets on a fluorocarbon-coated glass slide. Protein covariation analysis identifies cell cycle dynamics that are similar and dynamics that differ between cell types, even within subpopulations of melanoma cells delineated by markers for drug resistance priming. Melanoma cells expressing these markers accumulate in the G1 phase of the cell cycle, display distinct protein covariation across the cell cycle, accumulate glycogen, and have lower abundance of glycolytic enzymes. The non-primed melanoma cells exhibit gradients of protein abundance, suggesting transition states. Within this subpopulation, proteins functioning in oxidative phosphorylation covary with each other and inversely with proteins functioning in glycolysis. This protein covariation suggests divergent reliance on energy sources and its association with other biological functions. These results are validated by different mass spectrometry methods.

CONCLUSIONS

nPOP enables flexible, automated, and highly parallelized sample preparation for single-cell proteomics. This allows for quantifying protein covariation across thousands of single cells and revealing functionally concerted biological differences between closely related cell states. Support for nPOP is available at https://scp.slavovlab.net/nPOP .

Advances and enabling technologies for phase-specific cell cycle synchronisation

Cell cycle synchronisation is the process of isolating cell populations at specific phases of the cell cycle from heterogeneous, asynchronous cell cultures. The process has important implications in targeted gene-editing and drug efficacy of cells and in studying cell cycle events and regulatory mechanisms involved in the cell cycle progression of multiple cell species. Ideally, cell cycle synchrony techniques should be applicable for all cell types, maintain synchrony across multiple cell cycle events, maintain cell viability and be robust against metabolic and physiological perturbations. In this review, we categorize cell cycle synchronisation approaches and discuss their operational principles and performance efficiencies. We highlight the advances and technological development trends from conventional methods to the more recent microfluidics-based systems. Furthermore, we discuss the opportunities and challenges for implementing high throughput cell synchronisation and provide future perspectives on synchronisation platforms, specifically hybrid cell synchrony modalities, to allow the highest level of phase-specific synchrony possible with minimal alterations in diverse types of cell cultures.

The Anti-G0 Manifesto: Should a problematic construct (G0) with no biological reality be removed from the cell cycle? Yes!

It is widely accepted that there exists a "resting" or "quiescent" state where a growing cell leaves the cell cycle to enter what is often called the "G0-phase." I propose that there is no biological reality to the "G0-phase." The experimental basis for proposing a G0-phase is re-examined and re-analyzed here showing that the G0-phase is an anthropomorphic construct with no biological reality.

FRET-Based Sorting of Live Cells Reveals Shifted Balance between PLK1 and CDK1 Activities During Checkpoint Recovery

Cells recovering from the G2/M DNA damage checkpoint rely more on Aurora A-PLK1 signaling than cells progressing through an unperturbed G2 phase, but the reason for this discrepancy is not known. Here, we devised a method based on a FRET reporter for PLK1 activity to sort cells in distinct populations within G2 phase. We employed mass spectroscopy to characterize changes in protein levels through an unperturbed G2 phase and validated that ATAD2 levels decrease in a proteasome-dependent manner. Comparing unperturbed cells with cells recovering from DNA damage, we note that at similar PLK1 activities, recovering cells contain higher levels of Cyclin B1 and increased phosphorylation of CDK1 targets. The increased Cyclin B1 levels are due to continuous Cyclin B1 production during a DNA damage response and are sustained until mitosis. Whereas partial inhibition of PLK1 suppresses mitotic entry more efficiently when cells recover from a checkpoint, partial inhibition of CDK1 suppresses mitotic entry more efficiently in unperturbed cells. Our findings provide a resource for proteome changes during G2 phase, show that the mitotic entry network is rewired during a DNA damage response, and suggest that the bottleneck for mitotic entry shifts from CDK1 to PLK1 after DNA damage.

Cell Cycle Synchronization of the Murine EO771 Cell Line Using Double Thymidine Block Treatment

This study shows that double thymidine block treatment efficiently arrests the EO771 cells in the S-phase without altering cell growth or survival. A long-term analysis of cell behavior, using 5(6)-carboxyfluorescein diacetate N-succinimidyl ester (CFSE) staining, show synchronization to be stable and consistent over time. The EO771 cell line is a medullary breast-adenocarcinoma cell line isolated from a spontaneous murine mammary tumor, and can be used to generate murine tumor implantation models. Different biological (serum or amino acid deprivation), physical (elutriation, mitotic shake-off), or chemical (colchicine, nocodazole, thymidine) treatments are widely used for cell synchronization. Of the different methods tested, the double thymidine block is the most efficient for synchronization of murine EO771 cells if a large quantity of highly synchronized cells is recommended to study functional and biochemical events occurring in specific points of cell cycle progression.