Biology subjects

Khetan, N.

Publications and source records attributed to Khetan, N..

8 recordsLinked to original sources

bioRxiv2026

A genetic switch involving EGR1 and EZH2 links aging and development across human tissues

Aging is often regarded as the last chapter of development. There is growing evidence that aging and development are mechanistically linked. Here we describe a genetic switch involving EZH2 and EGR1 as opposing regulatory nodes that appears to connect aging and development across human tissues. We show that this switch defines two distinct states in fibroblasts: a proliferative (EZH2-high/EGR1-low) state and a non-proliferative and extracellular matrix-expressing (EGR1-high/EZH2-low) state. During replicative aging, cells shift from the proliferative state to the non-proliferative state and targeting either regulatory node--by overexpressing EZH2 or suppressing EGR1--rejuvenates aged fibroblasts. We provide evidence that this switch is involved in the transition from neural progenitor cells to matured neurons during brain development and becomes destabilized during aging, partially reversing the gene expression program established during development. We observed that this same switch becomes blurred and biased towards EGR1-high/EZH2-low state during the aging of muscle stem cells and hematopoietic stem cells. Since genetic switches are widely used in development to establish and reinforce cellular identity, we propose that attenuation of developmental switches may underlie aging across diverse organs and tissues, and partially accounts for the erosion of the epigenetic landscape and the loss of cellular identity.

systems biology↗

bioRxiv2026

Preferential formation of NUP98-KDM5A condensates at specific H3K4me3-rich loci drives leukemogenic gene expression

Chromosomal translocations involving NUP98 generate fusion proteins that alter gene expression programs, yet the fundamental principles governing their gene targeting and condensate behavior remain poorly understood. Using NUP98-KDM5A as a model, we integrate cellular imaging, in vitro reconstitution, and genomic analyses to dissect how chromatin engagement shapes condensate formation. We find that NUP98-KDM5A forms sub-diffraction-limited, gel-like condensates whose assembly is potentiated by binding to H3K4me3. This interaction creates a quantitative targeting mechanism in which, at the native expression level, condensates preferentially form at genomic loci with high local H3K4me3 density. Such local density-dependent recruitment explains selective enrichment at the leukemogenic HOX gene clusters, despite widespread presence of H3K4me3 across the genome. Analysis of single-cell sequencing data from patients further supports a correlation between local H3K4me3 density and transcriptional activation in NUP98-KDM5A-driven leukemia. Together, our findings reveal how activating chromatin marks and condensate-forming proteins synergize to generate specificity within euchromatin, offering a generalizable framework for understanding how chromatin-associated condensates interpret epigenetic landscapes.

cell biology↗

bioRxiv2026

Limitations of inferring antiviral efficacy of interfering particles from observational natural histories

Recently Hariharan et al.2 reported naturally arising defective HIV genomes capable of conditional replication and interference in humans. While this work makes an important contribution to the field of therapeutic interfering particles (TIPs), particularly with respect to safety and tolerability, it also raises fundamental issues regarding: (i) whether the presented data constitute a valid test of, or support conclusions about, the therapeutic potential of TIPs and (ii) technical issues pertaining to the reported basic reproductive numbers (R0). Hariharan et al. conclude that the findings "raise concerns about the effectiveness of TIPs." However, the data presented do not constitute a valid test of therapeutic efficacy. Here, we (i) clarify that post-hoc observational natural history cannot adjudicate the success or failure of an intervention, (ii) show new analysis highlighting how the reported R0 measurements are internally inconsistent with the within-host viral dynamics reported, and (iii) explain that alternative, well-established mechanisms remain sufficient to explain the reported observations.

microbiology↗

bioRxiv2024

Quantitative comparison of single-cell RNA sequencing versus single-molecule RNA imaging for quantifying transcriptional noise

Stochastic fluctuations (noise) in transcription generate substantial cell-to-cell variability. However, how best to quantify genome-wide noise, remains unclear. Here we utilize a small-molecule perturbation (IdU) to amplify noise and assess noise quantification from numerous scRNA-seq algorithms on human and mouse datasets, and then compare to noise quantification from single-molecule RNA FISH (smFISH) for a panel of representative genes. We find that various scRNA-seq analyses report amplified noise, without altered mean-expression levels, for [~]90% of genes and that smFISH analysis verifies noise amplification for the vast majority of genes tested. Collectively, the analyses suggest that most scRNA-seq algorithms are appropriate for quantifying noise including a simple normalization approach, although all of these systematically underestimate noise compared to smFISH. From a practical standpoint, this analysis argues that IdU is a globally penetrant noise-enhancer molecule--amplifying noise without altering mean-expression levels--which could enable investigations of the physiological impacts of transcriptional noise. MOTIVATIONCell-to-cell variability in isogenic populations is predominantly attributed to the stochastic fluctuations (i.e., noise) in transcription. However, the quantification of this noise, particularly on a genome-wide scale, remains an open question. To address this general question, here we utilize a small-molecule perturbation reported to amplify transcriptional noise. Previous single-cell RNA-sequencing (scRNA-seq) analysis indicated that the pyrimidine nucleobase 5'-iodo-2'-deoxyuridine (IdU) amplifies noise but technical drawbacks of scRNA-seq may have obscured the penetrance and degree of noise amplification. Consequently, here we assess numerous scRNA-seq algorithms, on two different scRNA-seq datasets for a human and mouse cell type, for their ability to quantify noise amplification and then compare the results to noise quantification from single-molecule RNA FISH (smFISH) imaging for a panel of representative genes. The specific questions addressed are whether IdU amplifies noise in a globally or partially penetrant manner, and what scRNA-seq algorithm is most appropriate for quantifying transcriptional noise. O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/607289v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1f9b17aorg.highwire.dtl.DTLVardef@1f2d410org.highwire.dtl.DTLVardef@1407cfaorg.highwire.dtl.DTLVardef@cd2bc9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

systems biology↗

bioRxiv2022

Emergence of flagella-like oscillations in single microtubules driven by collective dynein transport

Flagellar and ciliary oscillations result from a combination of stereotypical axonemal geometry, collective mechanics of motors, microtubules (MTs), elastic linkers and biochemical regulation. However, the minimal essential components and constraints resulting in flagellar oscillations remain unclear. Here, we demonstrate that periodic, low-frequency waves of flagella-like oscillations in vitro emerge from a ATP-driven collective molecular motor transport of MTs clamped at one end. The spontaneous oscillations arise without any external forcing and can be explained by an in silico model of molecular motor binding driven MT bending and buckling followed by motor detachment driven recovery stroke. We demonstrate that transitions in single MT patterns between flapping, flagellar-beating and looping are determined solely by the self-organization of collective motor transport and filament elasticity.

biophysics↗

bioRxiv2020

Dynein collective behavior in mitotic nuclear positioning of Saccharomyces cerevisiae

1Positioning the nucleus at the bud-neck prior during Saccharomyces cerevisiae mitosis during anaphase involves pulling forces of cytoplasmic dynein localized in the daughter cell. While genetic analysis has revealed a complex network positioning the nucleus, quantification of the forces acting on the nucleus and dyneins numbers driving the process has remained difficult. In order to better understand the role of motor-microtubule mechanics during nuclear positioning and the role of dynein, we have used a computational model of nuclear mobility in S. cerevisiae and reconciled it to the mobility of labelled spindle pole bodies (SPBs) measured by quantifying fluorescence microscopy time-series. We model the apparent random-walk mobility of SPBs by combining diffusion of the nucleus and active pushing of MTs at the cell membrane. By minimizing the deviation between tracks of fluorescently tagged SPBs and simulations, we estimate the effective cytoplasmic viscosity to be 0.5 Pa s. The directed transport of nuclei during the budding process is similarly quantified by tracking the daughter SPB (SPB-D) in experiment. Using force-balance, we find 2 to 8 motors are required to pull the nucleus to the bud-neck. Simulations of the cytoplasmic MT (cMT) search and capture by dynein suggest single motor binding is followed by a rapid saturation of number of bound motors. The short time and length of MT interactions with the cortex and minimal collective dynein force required, predict a functional role for dynein clustering in nuclear positioning.

cell biology↗

bioRxiv2017

‘Switch-like’ transition from random to directed motility of microtubules by a yeast dynein

Processive transport by multiple molecular motors that step stochastically, requires a form of mechanical coupling. In a quantitative microtubule (MT) gliding assay with yeast cytoplasmic dynein, we investigate the nature of this coupling by examining the effect of MT length and motor density on transport. We find speed and velocity have a length dependence for low motor numbers, but are independent of MT length for high motor densities. The dependence of speed, velocity and degree of randomness of MT transport is best understood when evaluated in terms of the numbers of motors bound to a filament. A model of collective transport of MTs, based on stochastic stepping and asymmetric detachment rates, reproduces the experimental trends of decreasing diffusivity with increasing number of motors. Additionally, the model predicts a switch-like increase in directionality of MT transport above a threshold number of motors. Such a rapid transition from random to directed motility with increasing numbers of yeast dyneins, could play a role in vivo during mitosis in the search and orientation of the Saccharomyces cerevisiae nucleus.

biophysics↗

bioRxiv2017

Mechanics of Hydra Detachment from Subrates: The Role of Substrate Rigidity and Starvation

Hydra is a fresh water hydrozoan living as a solitary polyp with a sedentary feeder lifestyle attached to a substrate. In times of food shortage they are reported to detach from their substrate and move either by drifting or somer-saulting. The attachment to the substrate is usually by the basal-body which secretes a mucosal adhesive. The mechanical strength of the adhesion of Hydra has not been quantified so far. Here, we measure the force required to detach Hydra vulgaris and Hydra magnipapillata from a surface and the role of physical and physiological factors. In order to do this, we have developed a flow chamber with a calibrated jet of water. We find H. vulgaris adhering to a hard substrate - a glass cover slip- requires more force to detach it as compared to a soft substrate- polyacrylamide gel. While H. vulgaris after one week of starvation detaches with very similar values of stress, H. magnipapillata detaches more readily when starved. These results suggest that the strength of adhesion is strongly affected by the stiffness of the substrate, while nutritional status dependence of detachment force appears to be species dependent. Given that Hydra detachment is required during locomotion, our measurements on the one hand suggest the magnitude of forces the animal must exert to detach itself. Additionally, our results suggest active detachment of the base might be required for Hydra to achieve movement, and only a small contribution coming from weakening adhesion.

biophysics↗