Biology subjects

Pines, J.

Publications and source records attributed to Pines, J..

8 recordsLinked to original sources

bioRxiv2026

Engineering and characterisation of AAVS1 FRT cell lines for inducible and dose-dependent gene expression

Investigating biological function with high reproducibility requires the generation of stable cell lines that offer precise and inducible transgene expression. However, traditional methods often suffer from the limitations of random genomic integration, including unpredictable expression levels, leaky basal activity, and disruption of endogenous loci. To address these challenges, we engineered a versatile RPE1 cell line by integrating a TetOn3G-FRT cassette into the AAVS1 safe-harbour locus using CRISPR/Cas9(D10A) nickase. This platform utilises the Flp-FRT recombination system to facilitate rapid, site-specific "plug-and-play" insertion of transgenes, combined with the Tet-On 3G system for tight, dose-dependent expression control. The resulting RPE1 AAVS1 FRT8 line enables highly consistent transgene induction across independent clones, behaving as a monoclonal population. We highlight the importance of rigorous cell line characterisation through a multi-omics approach. Whole genome sequencing identified precise heterozygous integration at the target locus and de novo genomic duplications on other chromosomes. By integrating WGS with high-resolution proteomics and cell cycle analysis, we confirmed that these alterations did not significantly perturb cellular homeostasis or phenotypic fitness. This work establishes a robust and reliable platform for the efficient generation of inducible AAVS1 FRT stable cell lines, facilitating reproducible research in modern molecular biology.

bioengineering↗

bioRxiv2026

Rapid early degradation of Cyclin A is important to maintain genomic stability

The Anaphase Promoting Complex/Cyclosome (APC/C) ubiquitin ligase controls mitosis by targeting the mitotic Cyclins for degradation. At Nuclear Envelope Breakdown the APC/C immediately targets CyclinA but the Spindle Assembly Checkpoint prevents it recognising CyclinB until all chromosomes have attached to the mitotic apparatus. The degradation of CyclinA before CyclinB is conserved in evolution but the physiological role of this is not yet clearly established. Overexpressing CyclinA or a non-degradable mutant interferes with chromosome congression and promotes microtubule instability, but the effect of delaying the degradation of endogenous CyclinA has not been determined. Here, we mutated two APC/C-recognition motifs in human CyclinA2 to slow down its degradation. We find that slower degradation of CyclinA alters microtubule dynamics and induces errors in chromosome congression and chromosome clustering at mitotic exit, leading to aneuploidy and malformed daughter cell nuclei. We identify Ki67 as the candidate to interfere with chromosome clustering since its phosphorylation and behaviour are perturbed when CyclinA is degraded more slowly. We conclude that rapid early CyclinA degradation is important for genomic stability.

cell biology↗

bioRxiv2026

Mechanistic basis for the spatiotemporal assembly of the Bloom Syndrome complex on ultrafine DNA bridges

The BTRR (BLM/TOP3A/RMI1/RMI2) complex resolves DNA replication and recombination intermediates, as well as mitotic DNA intertwinements, yet how its diverse activities are regulated remains unclear. Here, we identify key determinants of stable assembly of the BTRR complex on ultrafine DNA bridges (UFBs). We reveal that the RMI1-RMI2 subcomplex acts as a molecular reader of hydrophobic-rich short linear motifs (SLiMs) embedded within PICH and FANCM, thereby providing a conserved mechanism for engaging distinct Superfamily2 DNA translocases during chromosome segregation and DNA repair. During UFB resolution, SLiM binding stabilises the PICH-BTRR complex assembly and supports essential interactions among BLM, PICH, and DNA. Persistent PICH-BTRR complex association post-mitosis would compromise interphase DNA damage responses and is prevented by active PICH nuclear exclusion. Our findings define the molecular basis of UFB-binding complex assembly and highlight its spatiotemporal control required to specialise BTRR complex functions.

cell biology↗

bioRxiv2025

Single kinetochores execute an ordered series of molecular events as the Spindle Assembly Checkpoint is silenced

The Spindle Assembly Checkpoint (SAC) delays anaphase onset until all kinetochores are stably attached to microtubules, thus promoting error-free chromosome segregation. Multiple molecular events are implicated in SAC silencing, including removal of phospho-marks, protein (un)binding, and structural reorganisation of the kinetochore - but we currently lack a quantitative map of how these events unfold through time. Here, we use the levels of the checkpoint protein MAD2 to create a pseudo-timeline of SAC silencing at single kinetochores. We demonstrate how silencing proceeds through an ordered series of molecular events where MAD2-Spindly unbinds first and then the KNL1 catalytic platform disassembles, with a pool of active MPS1 retained. Coincidently, the NDC80 ensemble reconfigures in response to high microtubule occupancy. Kinetochores next switch into a mature attachment state that then undergoes gradual further stabilisation through NDC80 tail dephosphorylation. By preventing biorientation, we also define otherwise hidden kinetochore states involved in error correction cycles. This includes a "poised" state which we propose allows for error correction and rapid reactivation of the SAC. These results provide a critical temporal framework for understanding the mechanisms of SAC silencing and error correction at single human kinetochores.

cell biology↗

bioRxiv2024

High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells

The cell cycle governs a precise series of molecular events, regulated by coordinated changes in protein and phosphorylation abundance, that culminates in the generation of two daughter cells. Here, we present a proteomic and phosphoproteomic analysis of the human cell cycle in hTERT-RPE-1 cells using deep quantitative mass spectrometry by isobaric labelling. Through analysing non-transformed cells, and improving the temporal resolution and coverage of key cell cycle regulators, we present a dataset of cell cycle-dependent protein and phosphorylation site oscillation that offers a foundational reference for investigating cell cycle regulation. These data reveal uncharacterised regulatory intricacies including proteins and phosphorylation sites exhibiting previously unreported cell cycle-dependent oscillation, and novel proteins targeted for degradation during mitotic exit. Integrated with complementary resources, our data link cycle-dependent abundance dynamics to functional changes and are accessible through the Cell Cycle database (CCdb), an interactive web-based resource for the cell cycle community. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/599917v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@bb2a69org.highwire.dtl.DTLVardef@1dd55ecorg.highwire.dtl.DTLVardef@34073eorg.highwire.dtl.DTLVardef@1c7a8c9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Spatial control of the APC/C ensures the rapid degradation of Cyclin B1

The proper control of mitosis depends on the ubiquitin-mediated degradation of the right mitotic regulator at the right time. This is under the control of the anaphase promoting complex/cyclosome (APC/C) ubiquitin ligase that is regulated by the Spindle Assembly Checkpoint (SAC). The Checkpoint prevents the APC/C from recognizing Cyclin B1, the essential anaphase and cytokinesis inhibitor, until all chromosomes are attached to the spindle. Once chromosomes are attached, Cyclin B1 is rapidly degraded to enable chromosome segregation and cytokinesis. We have a good understanding of how the SAC inhibits the APC/C, but relatively little is known about how the APC/C recognises Cyclin B1 as soon as the SAC is turned off. Here, by combining live cell imaging, in vitro reconstitution, biochemistry, and structural analysis by cryo-electron microscopy, we provide evidence that the rapid recognition of Cyclin B1 in metaphase requires spatial regulation of the APC/C. Using fluorescence cross correlation spectroscopy, we find that Cyclin B1 and the APC/C primarily interact at the mitotic apparatus. We further show that this is because Cyclin B1, like the APC/C, binds to nucleosomes, and identify an arginine-anchor in the N-terminus as necessary and sufficient for binding to the nucleosome. Mutating the nucleosome binding motif on Cyclin B1 reduces its interaction with APC/C and delays its degradation, and cells with the mutant, non-nucleosome-binding Cyclin B1 become aneuploid, demonstrating the physiological relevance of our findings. Together, our data demonstrate that mitotic chromosomes constitute a platform to promote the efficient interaction between Cyclin B1 and APC/C and ensure the timely degradation of Cyclin B1 and genomic stability.

cell biology↗

bioRxiv2022

Cell cycle-dependent binding between Cyclin B1 and Cdk1 revealed by time-resolved Fluorescence Correlation Spectroscopy

Measuring the dynamics with which the regulatory complexes of the cell cycle machinery assemble and disassemble is a crucial barrier to our understanding that until now has been difficult to address. This considerable gap in our understanding is due to the difficulty of reconciling biochemical assays with single cell-based techniques, but recent advances in microscopy and gene editing techniques now enable the measurement of protein-protein interaction kinetics in living cells. Here, we apply Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Cross-Correlation Spectroscopy (FCCS) to study the dynamics of the cell cycle machinery, beginning with Cyclin B1 and its binding to its partner kinase Cdk1 that together form the major mitotic kinase. Although Cyclin B1 and Cdk1 are known to bind with high affinity, our results reveal that in living cells there is a pool of Cyclin B1 that is not bound to Cdk1. Furthermore, we provide evidence that the affinity of Cyclin B1 for Cdk1 increases during the cell cycle, indicating that the assembly of the complex is a regulated step. Our work lays the groundwork for studying the kinetics of protein complex assembly and disassembly during the cell cycle in living cells.

cell biology↗

bioRxiv2019

Cyclin B1-Cdk1 binding to MAD1 links nuclear pore disassembly to chromosomal stability

How the cell completely reorganises its architecture when it divides is a problem that has fascinated researchers for almost 150 years. We now know that the core regulatory machinery is highly conserved in eukaryotes but how these multiple protein kinases, protein phosphatases, and ubiquitin ligases are coordinated to remodel the cell in a matter of minutes remains a major question. Cyclin B-CDK is the primary kinase that drives mitotic remodelling and here we show that it is targeted to the nuclear pore complex (NPC) by binding an acidic face of the spindle assembly checkpoint protein, MAD1. This localised Cyclin B1-CDK1 activity coordinates NPC disassembly with kinetochore assembly: it is needed for the proper release of MAD1 from the embrace of TPR at the nuclear pore, which enables MAD1 to be recruited to kinetochores before nuclear envelope breakdown, thereby strengthening the spindle assembly checkpoint to maintain genomic stability.

cell biology↗