@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 {161318, title = {Paused RNA polymerase primes promoters via RNA-mediated stabilisation of transcription factor ERα.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Oct 29}, pages = {9553}, abstract = {

Regulated pausing of RNA polymerase II (Pol II) is essential for enabling rapid and coordinated transcriptional responses to signalling cues.\ Pausing also contributes to the formation of nucleosome-free regions with the help of chromatin remodellers. However, if these nucleosome-free regions engage with transcription factors to stimulate the transcription potential of paused promoters is not known. In this study, we demonstrate that ligand-induced estrogen receptor-alpha (ERα) binding is stabilized at Pol II-paused sites. This stabilization results from an increased dwell time of ERα on chromatin, as revealed by single molecule tracking (SMT) experiments. Notably, short chromatin-associated RNAs generated by the paused Pol II contribute to enhancing ERα binding at paused promoters. We also observe that pausing increases H3K27ac levels, which primes paused promoters for robust transcriptional activation upon release. Collectively, these findings suggest that paused Pol II plays a central role in enhancing transcription factor binding through an RNA-dependent mechanism. This, in turn, results in a more vigorous transcriptional response following pausing release, thus contributing to the fine-tuning of ERα-mediated gene regulation.

}, keywords = {Chromatin, Estrogen Receptor alpha, Histones, Humans, Nucleosomes, Promoter Regions, Genetic, Protein Binding, RNA, RNA Polymerase II, Transcription, Genetic, Transcriptional Activation}, issn = {2041-1723}, doi = {10.1038/s41467-025-64569-7}, author = {Mann, Rajat and Soota, Deepanshu and Das, Ayan and Podh, Nitesh Kumar and Mehta, Gunjan and Notani, Dimple} } @article {128080, title = {Transcription factor condensates and signaling driven transcription.}, journal = {Nucleus}, volume = {14}, year = {2023}, month = {2023 Dec}, pages = {2205758}, abstract = {

Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the 3D nuclear space is believed to provide a fast response, which is on the same pace as the signaling cascade and yet ever-so-specific in the crowded environment of the nucleus. However, the current understanding of how TF-condensates can achieve these feet so quickly and efficiently is still unclear. In this review, we draw parallels with other protein condensates and share our speculations on how the nucleus uses these TF-condensates to achieve high transcriptional specificity and fidelity. We discuss the various constituents of TF-condensates, their properties, and the known and unknown functions of TF-condensates with a particular focus on steroid signaling-induced transcriptional programs.

}, keywords = {Cell Nucleus, Chromatin, DNA, Signal Transduction, Transcription Factors}, issn = {1949-1042}, doi = {10.1080/19491034.2023.2205758}, author = {Mann, Rajat and Notani, Dimple} }