@article {161132, title = {Immunofluorescence Staining and Microscopic Imaging of Plant Nuclei for Epigenetic Modifications.}, journal = {Methods Mol Biol}, volume = {2988}, year = {2026}, month = {2026}, pages = {83-92}, abstract = {

Histone posttranslational modifications (PTMs) and DNA methylation are the predominant epigenetic modifications on the chromatin that regulate gene expression. These modifications can be spatially resolved using microscopic examination of the nuclei with the help of commercially available antibodies. Here, we describe a detailed method to obtain intact nuclei from plant tissues and reproducibly immunostain the nuclei for specific chromatin marks and microscopic examination. This method can be readily extended to multiple plant species as the antibodies are raised against conserved epigenetic marks.

}, keywords = {Cell Nucleus, Chromatin, DNA Methylation, Epigenesis, Genetic, Epigenomics, Fluorescent Antibody Technique, Histones, Microscopy, Fluorescence, Plants, Protein Processing, Post-Translational}, issn = {1940-6029}, doi = {10.1007/978-1-0716-4981-7_8}, author = {Gandhivel, Vivek Hari-Sundar and Raju, Steffi and Shivaprasad, P V} } @article {161131, title = {Targeted Bisulfite Sequencing and DNA Methylation Analysis in Rice Endosperm and Other Tissues.}, journal = {Methods Mol Biol}, volume = {2988}, year = {2026}, month = {2026}, pages = {71-82}, abstract = {

DNA methylation is a major epigenetic mark on chromatin. Tissue-specific DNA methylation in the regulatory regions of key genes modulates their tissue-specific expression. To study DNA methylation levels at specific sequence contexts across tissues or during various environmental conditions, whole-genome DNA methylation analysis is widely used. However, whole-genome methylation analysis is an expensive, time-consuming technique and requires specific skills. To understand the role of DNA methylation in a small number of candidate loci, targeted bisulfite (BS) PCR-sequencing analysis is an attractive option. Here, we describe a detailed method to understand DNA methylation by targeted-BS PCR analysis using rice endosperm tissues. This method can be readily extended to multiple monocots, across various tissues and various stress conditions.

}, keywords = {DNA Methylation, DNA, Plant, Endosperm, Epigenesis, Genetic, Genome, Plant, High-Throughput Nucleotide Sequencing, Oryza, Polymerase Chain Reaction, Sequence Analysis, DNA, Sulfites}, issn = {1940-6029}, doi = {10.1007/978-1-0716-4981-7_7}, author = {Pal, Avik Kumar and Gandhivel, Vivek Hari-Sundar and Shivaprasad, P V} } @article {152152, title = {NSD3 protein methylation and stabilization transforms human ES cells into variant state.}, journal = {Life Sci Alliance}, volume = {8}, year = {2025}, month = {2025 Mar}, abstract = {

Cultured human embryonic stem cells (hESCs) can develop genetic anomalies that increase their susceptibility to transformation. In this study, we characterized a variant hESC (vhESC) line and investigated the molecular mechanisms leading to the drift towards a transformed state. Our findings revealed that vhESCs up-regulate EMT-specific markers, accelerate wound healing, exhibit compromised lineage differentiation, and retain pluripotency gene expression in teratomas. Furthermore, we discovered an altered epigenomic landscape and overexpression of the lysine methyltransferases EHMT1, EHMT2, and NSD group of proteins in vhESCs. Remarkably, depleting NSD3 oncogene reversed the molecular and phenotypic changes in vhESCs. We identified a detailed mechanism where EHMT2 interacts and methylates NSD3 at lysine 477, stabilizing its protein levels in vhESCs. In addition, we showed that NSD3 levels are regulated by protein degradation in hESCs, and its stabilization leads to the emergence of the variant state. Overall, our study identify that misregulation of NSD3 in pluripotent stem cells, through methylation-mediated abrogation of its protein degradation, drives hESCs towards oncogenic transformation.

}, keywords = {Cell Differentiation, Cell Line, Cell Transformation, Neoplastic, Epigenesis, Genetic, Epithelial-Mesenchymal Transition, Histone-Lysine N-Methyltransferase, Human Embryonic Stem Cells, Humans, Intracellular Signaling Peptides and Proteins, Methylation, Nuclear Proteins, Pluripotent Stem Cells, Protein Stability, Repressor Proteins}, issn = {2575-1077}, doi = {10.26508/lsa.202402871}, author = {Krishnamoorthy, Vignesh K and Hamdani, Fariha and Shukla, Pooja and Rao, Radhika Arasala and Anaitullah, Shaikh and Biligiri, Kriti Kestur and Kadumuri, Rajashekar Varma and Pothula, Purushotham Reddy and Chavali, Sreenivas and Rampalli, Shravanti} } @article {137346, title = {A theoretical perspective on Waddington{\textquoteright}s genetic assimilation experiments.}, journal = {Proc Natl Acad Sci U S A}, volume = {120}, year = {2023}, month = {2023 Dec 19}, pages = {e2309760120}, abstract = {

Genetic assimilation is the process by which a phenotype that is initially induced by an environmental stimulus becomes stably inherited in the absence of the stimulus after a few generations of selection. While the concept has attracted much debate after being introduced by C. H. Waddington 70 y ago, there have been few experiments to quantitatively characterize the phenomenon. Here, we revisit and organize the results of Waddington{\textquoteright}s original experiments and follow-up studies that attempted to replicate his results. We then present a theoretical model to illustrate the process of genetic assimilation and highlight several aspects that we think require further quantitative studies, including the gradual increase of penetrance, the statistics of delay in assimilation, and the frequency of unviability during selection. Our model captures Waddington{\textquoteright}s picture of developmental paths in a canalized landscape using a stochastic dynamical system with alternative trajectories that can be controlled by either external signals or internal variables. It also reconciles two descriptions of the phenomenon-Waddington{\textquoteright}s, expressed in terms of an individual organism{\textquoteright}s developmental paths, and that of Bateman in terms of the population distribution crossing a hypothetical threshold. Our results provide theoretical insight into the concepts of canalization, phenotypic plasticity, and genetic assimilation.

}, keywords = {Adaptation, Physiological, Biological Evolution, Epigenesis, Genetic, Models, Genetic, Penetrance, Phenotype}, issn = {1091-6490}, doi = {10.1073/pnas.2309760120}, author = {Raju, Archishman and Xue, BingKan and Leibler, Stanislas} } @article {117962, title = {Initiation of wound healing is regulated by the convergence of mechanical and epigenetic cues.}, journal = {PLoS Biol}, volume = {20}, year = {2022}, month = {2022 Sep}, pages = {e3001777}, abstract = {

Wound healing in the skin is a complex physiological process that is a product of a cell state transition from homeostasis to repair. Mechanical cues are increasingly being recognized as important regulators of cellular reprogramming, but the mechanism by which it is translated to changes in gene expression and ultimately cellular behavior remains largely a mystery. To probe the molecular underpinnings of this phenomenon further, we used the down-regulation of caspase-8 as a biomarker of a cell entering the wound healing program. We found that the wound-induced release of tension within the epidermis leads to the alteration of gene expression via the nuclear translocation of the DNA methyltransferase 3A (DNMT3a). This enzyme then methylates promoters of genes that are known to be down-regulated in response to wound stimuli as well as potentially novel players in the repair program. Overall, these findings illuminate the convergence of mechanical and epigenetic signaling modules that are important regulators of the transcriptome landscape required to initiate the tissue repair process in the differentiated layers of the epidermis.

}, keywords = {Biomarkers, Caspase 8, Cues, Epigenesis, Genetic, Wound Healing}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3001777}, author = {Bhatt, Tanay and Dey, Rakesh and Hegde, Akshay and Ketkar, Alhad Ashok and Pulianmackal, Ajai J and Deb, Ashim P and Rampalli, Shravanti and Jamora, Colin} }