Biology subjects

Kidiyoor, G. R.

Publications and source records attributed to Kidiyoor, G. R..

5 recordsLinked to original sources

bioRxiv2025

The Deformability of the Mammalian Cell Nucleus is Determined by the Identity of the Lamin Rod Domain

Lamins are nuclear intermediate filament proteins with diverse functions, ranging from organizing chromatin and regulating gene expression to providing structural support to the nucleus. Mammalian cells express two types of lamins, A-type and B-type, which, despite their similar structure and biochemical properties, exhibit distinct differences in expression, interaction partners, and function. One major difference is that A-type lamins have a significantly larger effect on the mechanical properties of the nucleus, which are crucial for protecting the nucleus from cytoskeletal forces, enabling cell migration through confined spaces, and contributing to cellular mechanotransduction. The molecular mechanism underlying this difference has remained unresolved. Here, we applied custom-developed biophysical and proteomic assays to lamin-deficient cell lines engineered to express specific full-length lamin proteins, lamin truncations, or chimeras combining domains from A- and B-type lamins, to systematically determine their contributions to nuclear mechanics. We found that although all expressed lamins contribute to the biophysical properties of the nuclear interior and confer some mechanical stability to the nuclear envelope, which is sufficient to protect the nuclear envelope from small cell-intrinsic forces and ensure proper positioning of nuclear pores, A-type lamins endow cells with a unique ability to resist large forces on the nucleus. Surprisingly, this effect was conferred through the A-type lamin rod domain, rather than the head or tail domains, which diverge more substantially between A- and B-type lamins and play important roles in lamin network formation. Collectively, our work provides an improved understanding of the distinct functions of different lamins in mammalian cells and may also explain why mutations in the A-type lamin rod domain cause more severe muscle defects in mouse models than other mutations.

cell biology↗

bioRxiv2025

Herpes simplex virus-1 fluidizes the nucleus enabling condensate formation

Molecular processes are profoundly influenced by the biophysical properties of the cell interior. However, the mechanisms that control these physical properties, and the processes they impact remain poorly understood, especially in the nucleus. We hypothesized that some viruses might change the biophysical properties of the nucleus to favor virus survival and replication and found that herpes simplex virus 1 (HSV-1) increases the mesoscale fluidity of the nucleus. The HSV-1 protein ICP4 caused fluidization and enabled growth of synthetic nuclear condensates. Conversely, conditions that decreased nuclear fluidity inhibited the growth of viral replication compartment condensates and reduced infectious virus production. Together, our data suggest that ICP4 increases nuclear fluidity to promote the formation of condensates that drive the progression of the HSV-1 life cycle. We speculate that a key function of ICP4 is to overcome the crowding and elastic confinement within cell nuclei that are a fundamental barrier to virus replication.

cell biology↗

bioRxiv2023

KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells

Aneuploidy--the presence of chromosome gains and losses--is highly prevalent in human tumors, yet the contribution of chromosome missegregation rates and selection to shape these patterns remains poorly understood. To address this challenge at scale, we developed KaryoTap, a cost-effective single-cell DNA sequencing method combining custom targeted panels for the Tapestri platform with a Bayesian gaussian mixture model to detect chromosome- and chromosome arm-scale aneuploidy as well as integrated gRNAs and barcodes. KaryoTap achieves an average accuracy of >85% for arm events and >90% for chromosome events at <$1 per cell, allowing scalable analysis of tens of thousands of cells per experiment. Through KaryoTap-based analysis of 11,555 cells, we performed in vitro evolution screens on immortalized human cells from mammary gland, pancreas and melanocytes. By comparing aneuploidy frequencies immediately after reversine-induced missegregation versus after extended proliferation, we quantified positive and negative selection for specific aneuploidies. Most aneuploidies--both gains and losses--are under negative selection, yet some chromosomal gains are under positive selection (such as 8q and 7q). We found that proliferative selective pressures can explain tissue-specific patterns of chromosomal gains observed in human cancers. Critically, when positively selected events were excluded from analysis, correlations between in vitro and cancer gain frequencies strongly decreased or disappeared, whereas excluding negatively selected events largely preserved these correlations. These findings demonstrate that proliferative selection shapes the landscape of chromosomal gains in cancer, with a more prominent role for positive selection.

genomics↗

bioRxiv2021

Centripetal nuclear shape fluctuations associate with chromatin condensation towards mitosis

The cell nucleus plays a central role in several key cellular processes, including chromosome organisation, replication and transcription. Recent work intriguingly suggests an association between nuclear mechanics and cell-cycle progression, but many aspects of this connection remain unexplored. Here, by monitoring nuclear shape fluctuations at different cell cycle stages, we uncover increasing inward fluctuations in late G2 and early mitosis, which are initially transient, but develop into instabilities that culminate into nuclear-envelope breakdown in mitosis. Perturbation experiments and correlation analysis reveal an association of these processes with chromatin condensation. We propose that the contrasting forces between an extensile stress and centripetal pulling from chromatin condensation could link mechanically chromosome condensation and nuclear- envelope breakdown, the two main nuclear processes during mitosis. Significance StatementThe nucleus was recently shown to exhibit shape fluctuations that vary with cell-cycle stage, but we know very little about the possible links between nuclear mechanics and cell cycle- progression. Through flickering analysis, this study monitors radius and nuclear envelope fluctuations across the cell cycle. The authors discover that as the cell cycle progresses towards mitosis, localised inward invaginations of the nuclear shape form initially transiently and gradually increasing their amplitude, in association with chromatin condensation. This phenomenon develops into nuclear envelope breakdown, suggesting a novel link between cell cycle, chromatin mechanics and nuclear shape fluctuations.

biophysics↗

bioRxiv2021

nucGEMs probe the biophysical properties of the nucleoplasm

The cell interior is highly crowded and far from thermodynamic equilibrium. This environment can dramatically impact molecular motion and assembly, and therefore influence subcellular organization and biochemical reaction rates. These effects depend strongly on length-scale, with the least information available at the important mesoscale (10-100 nanometers), which corresponds to the size of crucial regulatory molecules such as RNA polymerase II. It has been challenging to study the mesoscale physical properties of the nucleoplasm because previous methods were labor-intensive and perturbative. Here, we report nuclear Genetically Encoded Multimeric nanoparticles (nucGEMs). Introduction of a single gene leads to continuous production and assembly of protein-based bright fluorescent nanoparticles of 40 nm diameter. We implemented nucGEMs in budding and fission yeast and in mammalian cell lines. We found differences in particle motility between the nucleus and the cytosol at the mesoscale, that mitotic chromosome condensation ejects nucGEMs from the nucleus, and that nucGEMs are excluded from heterochromatin and the nucleolus. nucGEMs enable hundreds of nuclear rheology experiments per hour, and allow evolutionary comparison of the physical properties of the cytosol and nucleoplasm.

biophysics↗