Biology subjects

Singh, A. A.

Publications and source records attributed to Singh, A. A..

4 recordsLinked to original sources

bioRxiv2026

Multiscale Physical Effects of CpG Methylation on DNA Mechanics, Nucleosome Wrapping, and Chromatin Condensates

DNA methylation at CpG dinucleotides is a central epigenetic modification linked to transcriptional repression and heterochromatin formation, yet its physical impact on chromatin organization remains incompletely understood. Here, we integrate single-molecule force spectroscopy, FRAP, and nanorheology to quantify how CpG methylation alters chromatin mechanics across scales. Optical tweezer-based measurements show that CpG methylation modestly increases DNA contour and persistence lengths, indicating a slightly extended and stiffer DNA helix. When assembled into nucleosomes, CpG methylation weakens both outer-and inner turn wrapping, reducing unwrapping forces and per-nucleosome unwrapping energy. On a higher-order assembly scale, although CpG methylated and unmethylated chromatin fibers display similar thresholds for salt-induced phase separation, methylated condensates exhibit markedly reduced internal mobility: FRAP reveals slower chromatin exchange, nanorheology shows increased viscoelasticity and longer relaxation times. Finally, CpG methylation enhances HP1-chromatin interactions, lowering the HP1 concentration required for condensation, despite no change in HP1 binding to naked DNA. Together, these results show that CpG methylation remodels chromatin mechanics by tuning DNA rigidity, nucleosome wrapping energetics, and condensate material properties, providing a multiscale physical framework for how DNA methylation contributes to heterochromatin.

biochemistry↗

bioRxiv2023

Coupling Cell Size Regulation and Proliferation Dynamics of C.glutamicum Reveals Cell Division Based on Surface Area

Single cells actively coordinate growth and division to regulate their size, yet how this size homeostasis at the single-cell level propagates over multiple generations to impact clonal expansion remains fundamentally unexplored. Classical timer models for cell proliferation (where the duration of the cell cycle is an independent variable) predict that the stochastic variation in colony size will increase over time. In stark contrast, implementing size control according to adder strategy (where on average a fixed size added from cell birth to division) leads to colony size variations that eventually decay to zero. While these results assume a fixed size of the colony-initiating progenitor cell, further analysis reveals that the magnitude of the intercolony variation in population number is sensitive to heterogeneity in the initial cell size. We validate these predictions by tracking the growth of isogenic microcolonies of Corynebacterium glutamicum in microfluidic chambers. Approximating their cell shape to a capsule, we observe that the degree of random variability in cell size is different depending on whether the cell size is quantified as per length, surface area, or volume, but size control remains an adder regardless of these size metrics. A comparison of the observed variability in the colony population with predictions suggests that proliferation matches better with a cell division based on the cell surface. In summary, our integrated mathematical-experimental approach bridges the paradigms of single-cell size regulation and clonal expansion at the population levels. This innovative approach provides elucidation of the mechanisms of size homeostasis from the stochastic dynamics of colony size for rod-shaped microbes.

systems biology↗

bioRxiv2023

Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and alterations in 3D genome organization to stimulate oncogene expression

The incidence and mortality of Endometrial Cancer (EC) is on the rise. 85% of ECs depend on Estrogen Receptor alpha (ER) for proliferation, but little is known about its transcriptional regulation in these tumors. We generated epigenomics, transcriptomics and Hi-C datastreams in healthy and tumor endometrial tissues, identifying robust ER reprogramming and profound alterations in 3D genome organization that lead to a gain of tumor-specific enhancer activity during EC development. Integration with endometrial cancer risk single-nucleotide polymorphisms, as well as WGS data from primary tumors and metastatic samples revealed a striking enrichment of risk variants and non-coding somatic mutations at tumor-enriched ER sites. Through machine learning-based predictions and interaction proteomics analyses, we identified an enhancer mutation which alters 3D genome conformation, impairing recruitment of the transcriptional repressor EHMT2/G9a/KMT1C, thereby alleviating transcriptional repression of ESR1 in EC. In summary, we identified a complex genomic-epigenomic interplay in EC development and progression, altering 3D genome organization to enhance expression of the critical driver ER.

cancer biology↗

bioRxiv2017

Comparative analysis of neutrophil and monocyte epigenomes

Neutrophils and monocytes provide a first line of defense against infections as part of the innate immune system. Here we report the integrated analysis of transcriptomic and epigenetic landscapes for circulating monocytes and neutrophils with the aim to enable downstream interpretation and functional validation of key regulatory elements in health and disease. We collected RNA-seq data, ChIP-seq of six histone modifications and of DNA methylation by bisulfite sequencing at base pair resolution from up to 6 individuals per cell type. Chromatin segmentation analyses suggested that monocytes have a higher number of cell-specific enhancer regions (4-fold) compared to neutrophils. This highly plastic epigenome is likely indicative of the greater differentiation potential of monocytes into macrophages, dendritic cells and osteoclasts. In contrast, most of the neutrophil-specific features tend to be characterized by repressed chromatin, reflective of their status as terminally differentiated cells. Enhancers were the regions where most of differences in DNA methylation between cells were observed, with monocyte-specific enhancers being generally hypomethylated. Monocytes show a substantially higher gene expression levels than neutrophils, in line with epigenomic analysis revealing that gene more active elements in monocytes. Our analyses suggest that the overexpression of c-Myc in monocytes and its binding to monocyte-specific enhancers could be an important contributor to these differences. Altogether, our study provides a comprehensive epigenetic chart of chromatin states in primary human neutrophils and monocytes, thus providing a valuable resource for studying the regulation of the human innate immune system.

genomics↗