Biology subjects

Das, A.

Publications and source records attributed to Das, A..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Fractal Measures as Predictors of Histopathological Complexity in Breast Carcinoma Mammograms

Breast carcinoma remains the most commonly diagnosed malignancy and a leading cause of cancer-related mortality among women worldwide. While mammography is the gold standard for early detection, challenges such as high breast density often obscure malignancies, reducing diagnostic sensitivity. Conventional parenchymal texture analysis methods have limitations due to struggles with spatial interpretation and noise sensitivity. This study investigates the efficacy of fractal-based global texture features for distinguishing between malignant and normal mammograms and assessing their potential for molecular subtype differentiation. Digital mammograms were analyzed using standardized preprocessing techniques, and fractal measures were computed to capture complexity and connectivity properties within breast tissue structures. Fractal dimension, multifractality strength, and succolarity reservoir were found to effectively characterize specific features of mammographic texture; however, their incorporation into machine learning models yielded moderate discriminatory performance between categories. We introduced succolarity reservoir as a novel parameter accounting for tissues latent connectivity. In addition, while succolarity reservoir exhibits potential for differentiating Luminal B from other molecular subtypes, its overall discriminative power remains limited. This proof-of-concept study underscores the potential of fractal-based texture analysis as a non-invasive biomarker in breast carcinoma diagnosis.

biophysics↗

bioRxiv2025

Inactivation of the Fusobacterium nucleatum Rnf complex reduces FadA-mediated amyloid formation and tumor development

The Gram-negative anaerobe Fusobacterium nucleatum is an oral oncobacterium that promotes colorectal cancer (CRC) development with the amyloid-forming cell surface adhesin FadA integral to CRC tumorigenesis. We describe here molecular genetic studies uncovering a novel mode of metabolic regulation of FadA-mediated tumor formation by a highly conserved respiratory enzyme known as the Rnf complex. First, we show that genetic disruption of Rnf, via rnfC deletion, significantly reduces the level of fadA transcript, accompanied by a near-complete abolishment of the precursor form of FadA (pFadA), reduced assembly of FadA at the mature cell pole, and severe defects in the osmotic stress-induced formation of FadA amyloids. We show further that the Rnf complex regulates three response regulators (CarR, ArlR, and S1), which modulate the expression of pFadA, without affecting fadA transcript. Consistent with our hypothesis that these response regulators control factors that process FadA, deletion of rnfC, carR, arlR, or s1 each impairs expression of the signal peptidase gene lepB, and FadA production is nearly abolished by CRISPR-induced depletion of lepB. Importantly, while rnfC deletion does not affect the ability of the mutant cells to adhere to CRC cells, rnfC deficiency significantly diminishes the fusobacterial invasion of CRC cells and formation of spheroid tumors in vitro. Evidently, the Rnf complex modulates the expression of the FadA adhesin and tumorigenesis through a gene regulatory network consisting of multiple response regulators, each controlling a signal peptidase that is critical for the post-translational processing of FadA and surface assembly of FadA amyloids. IMPORTANCEThe Rhodobacter nitrogen-fixation (Rnf) complex of Fusobacterium nucleatum plays an important role in the pathophysiology of this oral pathobiont, since genetic disruption of this conserved respiratory enzyme negatively impacts a wide range of metabolic pathways, as well as bacterial virulence in mice. Nonetheless, how Rnf deficiency weakens the virulence potential of F. nucleatum is not well understood. Here, we show that genetic disruption of the Rnf complex reduces surface assembly of adhesin FadA and FadA-mediated amyloid formation, via regulation of signal peptidase LepB by multiple response regulators. As FadA is critical in the carcinogenesis of colorectal cancer (CRC), the ability to invade CRC cells and promote spheroid tumor growth is strongly diminished in an Rnf-deficient mutant. Thus, this work uncovers a molecular linkage between the Rnf complex and LepB-regulated processing of FadA - likely via metabolic signaling - that maintains the virulence potential of this oncobacterium in various cellular niches.

microbiology↗

bioRxiv2025

Invasion blurs the biphasic mosaic, amplifies the 'wicked problem' through impacts on avian distributions in montane habitats.

Globally, managing invasive plants and habitat transformation often constitutes a wicked problem due to highly variable impacts on threatened biodiversity. In naturally patchy habitats, invasion can blur edges, pushing species beyond natural habitats. In biphasic habitats like forest-grassland mosaics, complementary sets of specialist species offer a unique configuration to examine such impacts from both directions. In the Shola Sky Islands, extensive woody invasive stands and agriculture/production landscapes have created a set of transformed closed and open habitats structurally similar to their natural counterparts. We expect the species usage of such novel habitats to reflect their dietary and habitat specialisation. We conducted 4,519 surveys across 1,204 randomly selected grid cells for the avian community, covering the global distribution of five species. For a select set of specialist and generalist species, we estimated patch occupancy and abundance using hierarchical models. We used acoustics to assess species persistence across invasion stages with automated recorders deployed across a year. We used community occurrence data to examine functional traits that correspond to habitat colonisation. Forest species occur year-round in transformed woody habitats across all invasion stages, and habitat overstory determines avian functional diversity. Forest specialists decline in transformed habitats across high-contrast edges, while generalists increase across both high- and low-contrast edges, indicating a supertramp strategy. Grassland specialist, however, decline strongly beyond all edges, creating a duality of losses and gains across the biphasic matrix. We highlight the diversity of threatened species responses to invasion and habitat transformation, underscoring the importance of nuanced approaches to habitat restoration, particularly in biphasic habitats.

ecology↗

bioRxiv2025

Downregulation of KRT proteins in the Neuroendocrine System of Amyotrophic Lateral Sclerosis with PT150 as a Multi-Target Neuroprotectant

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterized by motor neuron degeneration. Although ALS biomarkers exist, they lack specificity and early-onset. ALS also has a 40% misdiagnosis rate. This paper proposes the use of a Graph Neural Network (GNN) to diagnose ALS, new ALS-specific biomarkers, and a therapeutic based on this group. Gene expression and proteomic datasets were sourced. A kNN data representation was used to train a GNN for disease diagnosis. Achieving 98% accuracy between ALS and control, and 85% between ALS patients and ALS mimics (the specific diseases within this class were not disclosed), outperforming existing approaches. Integrated Gradients then quantified each genes importance in the models decision. KRTAP3-1 and KRTAP9-8 were substantial in the models classification process due to involvement in cytoskeletal organization. In parallel, statistical proteomi analysis revealed the significance of KRT6A, KRT6B, and KRT4 due to involvement in cytoskeletal organization, tissue development, and cellular differentiation, all related to ALS. These keratin proteins were expressed in the pituitary gland, suggesting that their downregulation contributes to hormonal dysregulation in ALS. Once Glucocorticoid Receptor (GR) was found to be the reason for keratin downregulation, molecular docking identified PT150 as a therapeutic, binding with and inhibiting GR and Cyclooxygenase 2, also reducing neuroinflammation in ALS.

systems biology↗

bioRxiv2025

The coronavirus helicase synergizes with the viral RNA polymerase to enable rapid RNA synthesis through duplex RNA

Positive-sense (+) RNA viruses often encode helicases presumed to support replication. Their precise role remains unresolved though, especially in coronaviruses (CoV) where the helicase translocates in the opposite direction to the polymerase. Using high-throughput single-molecule magnetic tweezers, we show that the coronavirus helicase enhances RNA synthesis through duplex RNA by tenfold, forming a directional complex with the viral polymerase. Despite opposing polarity, the helicase coordinates elongation by engaging the non-template strand. A detailed kinetic model derived from large datasets reveals distinct dynamic states, including fast bursting and slow, backtracking-prone modes, which are governed by helicase engagement. These results uncover an active coupling mechanism that modulates replication dynamics and provide a mechanistic basis for continuous versus discontinuous RNA synthesis in coronaviruses. Our findings establish the viral helicase as a central regulator of RNA replication rather than a passive accessory enzyme.

biophysics↗

bioRxiv2025

A prophage-encoded anti-phage defense system that prevents phage DNA packaging by targeting the terminase complex

A unique feature of temperate phages is the ability to protect their host bacteria from a second phage infection. Such protection is granted at the lysogenic state, where the phages persist as prophages integrated within the bacterial chromosome, expressing genes that defend the host and themselves from predation. Here, we report a prophage-encoded anti-phage defense system that inhibits DNA packaging of invading phages in Listeria monocytogenes. This system includes a defense protein, TerI, and two self-immunity proteins, anti-TerI1 and anti-TerI2. TerI targets the terminase complex of invading phages to prevent DNA translocation into procapsids without halting the lytic cycle, leading to the release of unpacked non-infectious procapsids upon bacterial lysis. In contrast, the self-immunity proteins, anti-TerI1 and anti-TerI2, counteract TerI during prophage induction to allow virion production. This unique prophage-encoded anti-phage defense system, TERi, is prevalent in Listeria phages, providing population-level host protection without compromising the prophage lytic lifecycle.

microbiology↗

bioRxiv2025

Optochemical control over mRNA translation by photocaged phosphorodiamidate morpholino oligonucleotides in vivo

A key regulatory step in protein synthesis is the initiation of mRNA translation. We developed an efficient, robust, and broadly applicable system for light-induced protein translation to control the production of proteins of interest and study their function. The method is based on the displacement of a single type of antisense morpholino from RNA by the uncaged guanidinium-linked morpholino (GMO)-phosphorodiamidate morpholino oligonucleotide (PMO) chimera upon UV irradiation. The GMO-PMO chimera designed here is cell-permeable and the GMO part can be produced employing a new mercury-free approach compatible with the synthesis on solid support. We demonstrate the function of this novel optochemical approach in live embryos by inducing, at desired times and locations, the expression of proteins that label specific cells, ablate tissue regions, and affect embryonic development. Together, our results demonstrate that the cell-permeable GMO-PMO chimera offers a unique strategy for controlling the function of mRNAs of interest. This method allows for the production of proteins at specific times and positions within live organisms, facilitating numerous applications in biomedical research and therapy.

developmental biology↗

bioRxiv2025

Assessment of critically endangered Northern River Terrapin (Batagur baska) phylogeny through next-generation sequencing-based mitogenome analyses

The Northern River Terrapin, Batagur baska (Gray, 1830), is a critically endangered freshwater turtle, primarily found in the estuaries and tidal regions of large rivers in South and Southeast Asia. B. baska has experienced extensive population declines and extirpations across most of its range, with no confirmed wild populations remaining. To support conservation efforts of this turtle, our study utilizes first complete mitochondrial genome of B. baska using next-generation sequencing (NGS). This mitochondrial genome data is combined with existing genetic information to evaluate the species phylogenetic position within the Geoemydidae family. The Bayesian phylogenetic analysis, including 38 species sequences, confirmed a close genetic relationship between B. baska and B. affinis (posterior probability = 1). The mitochondrial genome of B. baska consists of 16,503 base pairs, with a typical structure comprising 13 protein-coding genes, two rRNA genes, and 22 tRNA genes, along with a non-coding control region. The protein-coding genes account for 68.9% of the genome, while the ribosomal RNA and tRNA genes cover 15.4%. The control region, located between tRNAPro and tRNAPhe, is 986 bp long and exhibits a distinct base composition.

genomics↗

bioRxiv2025

Neuronal Silencing and Protection in a Mouse Model of Demyelination

Damage to the myelin sheath that protects axons in the central nervous system is a hallmark pathology of demyelinating diseases like multiple sclerosis. Cuprizone-induced demyelination in mice is a common model for studying demyelination and remyelination. However, the relationship between myelin damage and recovery and neuronal function remains poorly understood. By monitoring hippocampal myelination and neuronal activity in the same mice, we assessed longitudinal changes following cuprizone consumption and remyelination treatment. Upon cuprizone consumption, a rapid decline in neuronal activity preceded slower demyelination. Female mice showed a more intense early decrease in brain activity and a stronger correlation with levels of myelin loss. Remyelination treatment led to increased myelination levels and recovery of neuronal activity compared to vehicle treatment. Changes in single-neuron firing rates during treatment were proportional to the pre-cuprizone firing rate in the same cells, highlighting a potential linkage between the status of myelin recovery and cellular activity.

neuroscience↗

bioRxiv2025

Endothelial Cu Uptake Transporter CTR1 Senses Disturbed Flow to Promote Atherosclerosis through Cuproptosis

Endothelial cells (ECs) lining blood vessels sense disturbed blood flow (D-flow), which drives mitochondrial dysfunction and atherosclerosis. Copper (Cu) is an essential micronutrient, and its disruption of homeostasis has been implicated in atherosclerosis. Cellular Cu levels are tightly controlled by Cu transport proteins including the Cu importer CTR1. Cuproptosis is a recently discovered form of regulated cell death triggered by mitochondrial Cu accumulation, but its endogenous stimulants and role in atherosclerosis remain unknown. Using EC-specific CTR1-deficient mice and cultured ECs, we show that endothelial CTR1 responds to D-flow by increasing mitochondrial Cu levels through its interaction with the mitochondrial Cu transporter SLC25A3 at caveolae/lipid rafts. This leads to the aggregation of lipoylated mitochondrial proteins, mitochondrial dysfunction, and cuproptosis, thereby exacerbating atherosclerosis. Importantly, mitochondria-targeted Cu-chelating nanoparticles effectively mitigate D-flow-induced cuproptosis and atherosclerosis, highlighting the endothelial CTR1-SLC25A3-mitochondrial Cu axis as a potential therapeutic target.

cell biology↗

bioRxiv2025

Differential regulation of brain-specific molecular pathways is the reason for curcumin adult life-phase specific DAergic neuroprotection: Insights from ALSS Drosophila model of Parkinson disease

AbstractCurcumin (CU), a bioactive compound of turmeric, has been put forward as a "golden molecule" due to its anti-inflammatory, antioxidant, hepatoprotective, neuroprotective, and anti-cancer ability, as proven by research conducted over the decade and more. Our laboratory, developed an adult life stage specific (ALSS) Drosophila model of sporadic Parkinsons disease (PD), and for first time demonstrated that dopaminergic (DAergic) neuroprotective efficacy of curcumin is limited to health phase viz. adult-young life stage and is absent during transition phase viz. adult senior life stages when PD set in. This observation suggests the limitation of curcumin as a therapeutic agent for late-onset disorders like PD. Further, our laboratory also demonstrated that despite curcumins ability to sequester oxidative stress during both the adult life stages, neuroprotection and brain dopamine replenishment is granted only in health stages but not in a vulnerable transition stage, which prompted to put forward the hypothesis that the molecular target(s) of CU, may be absent or inadequate in the transition stage of aging brain. With this insight, the current study was implemented to analyse the life stage-specific differential regulation of multiple molecular players of neuro-integral pathways in brain of ALSS Drosophila model of PD with curcumin intervention. It is discovered that curcumin-mediated health phase-specific neuroprotection underlies the correction of an altered expression of 1. dFOXO, GADD45, Puc of Bsk-dFOXO stress response pathway, 2. Mfn2 of Mitochondrial dynamics 3. CncC, GCLC, Prx 2540 -1,2, Jafrac1, Prx3 of Phase II antioxidant defense system pathway. Further, it is discovered that significant aging-associated naturally altered expression of certain molecular targets exists, that may contribute to the limitation of curcumins DAergic neuroprotective efficacy during the adult-transition stage. This knowledge will help in developing altered therapeutic strategies for PD as molecular targets of curcumin are conserved among fly, mice and human.

neuroscience↗

bioRxiv2025

A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent

Coronaviruses (CoV) encode sixteen non-structural proteins (nsps), most of which form the replication-transcription complex (RTC). The RTC contains a core composed of one nsp12 RNA-dependent RNA polymerase (RdRp), two nsp8s and one nsp7. The core RTC recruits other nsps to synthesize all viral RNAs within the infected cell. While essential for viral replication, the mechanism by which the core RTC assembles into a processive polymerase remains poorly understood. We show that the core RTC preferentially assembles by first having nsp12-polymerase bind to the RNA template, followed by the subsequent association of nsp7 and nsp8. Once assembled on the RNA template, the core RTC requires hundreds of seconds to undergo a conformational change that enables processive elongation. In the absence of RNA, the (apo-)RTC requires several hours to adopt its elongation-competent conformation. We propose that this obligatory activation step facilitates the recruitment of additional nsps essential for efficient viral RNA synthesis and may represent a promising target for therapeutic interventions.

biophysics↗

bioRxiv2024

Breaking Boundaries: New locality records and a reassessment of the conservation status of the Khasi Hill Toad (Bufoides meghalayanus) endemic to Meghalaya, Northeast India

Bufoides meghalayanus is a Critically Endangered toad, endemic to East Khasi Hills, Meghalaya, Northeast India. This endemic toad was presumed to be restricted to just three locations, all within 1-2 km from one another around the type locality in Meghalaya. This article gives the first account of three previously unknown populations, extending the known geographic range of the species significantly. Additionally, we include the newly obtained molecular sequences of B. meghalayanus in a comprehensive molecular phylogeny with a note on its genetic and morphometric variations within these new populations and its congeneric members.

ecology↗

bioRxiv2024

14-3-3 epsilon inhibits premature centriole disengagement by inhibiting the activity of Plk1 and Separase.

The 14-3-3 protein family regulates several pathways in mammalian cells, including centrosome duplication. However, the precise mechanisms by which 14-3-3 paralogs regulate the centrosome cycle remain unclear. To identify the mechanisms by which 14-3-3{varepsilon} regulates centrosome duplication, we altered two conserved acidic residues in the 14-3-3{varepsilon} phospho-peptide-binding pocket that regulate complex formation and dissociation with the associated ligands, D127 and E134, to Alanine. Altering these residues to Alanine led to opposing effects on centrosome duplication; the D127A mutant inhibited centrosome duplication, while cells expressing the E134A mutant showed the presence of supernumerary centrosomes. We demonstrate that 14-3-3{varepsilon} does not inhibit centriole duplication, as reported for 14-3-3{gamma}, but inhibits centriole disengagement. Using a combination of pharmacological and genetic approaches, we demonstrate that 14-3-3{varepsilon} inhibits the activity of Plk1 and Separase, leading to disengagement defects that ultimately lead to decreased proliferation and cell death. Our work demonstrates that different 14-3-3 paralogs regulate different steps in the centrosome cycle, and disrupting complex formation between 14-3-3{varepsilon} and Plk1 or Separase could be a novel therapeutic strategy in tumor cells.

cell biology↗

bioRxiv2024

Systemic exposure to COVID-19 virus-like particles modulates firing patterns of cortical neurons in the living mouse brain

Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) causes a systemic infection that affects the central nervous system. We used virus-like particles (VLPs) to explore how exposure to the SARS-CoV-2 proteins affects brain activity patterns in wild-type (WT) mice and in mice that express the wild-type human tau protein (htau mice). VLP exposure elicited dose-dependent changes in corticosterone and distinct chemokine levels. Longitudinal two-photon microscopy recordings of primary somatosensory and motor cortex neurons that express the jGCaMP7s calcium sensor tracked modifications of neuronal activity patterns following exposure to VLPs. There was a substantial short-term increase in stimulus-evoked activity metrics in both WT and htau VLP-injected mice, while htau mice showed also increased spontaneous activity metrics and increase activity in the vehicle-injected group. Over the following weeks, activity metrics in WT mice subsided, but remained above baseline levels. For htau mice, activity metrics either remain elevated or decreased to lower levels than baseline. Overall, our data suggest that exposure to the SARS-CoV-2 VLPs leads to strong short-term disruption of cortical activity patterns in mice with long-term residual effects. The htau mice, which have a more vulnerable genetic background, exhibited more severe pathobiology that may lead to more adverse outcomes.

neuroscience↗

bioRxiv2024

Ethanolamine-induced assembly of microcompartments is required for Fusobacterium nucleatum virulence

Many bacteria metabolize ethanolamine as a nutrient source through cytoplasmic organelles named bacterial microcompartments (BMCs). Here we investigated the molecular assembly, regulation, and function of BMCs in Fusobacterium nucleatum - a Gram-negative oral pathobiont that is associated with adverse pregnancy outcomes. The F. nucleatum genome harbors a conserved ethanolamine utilization (eut) locus with 21 genes that encode several putative BMC shell proteins and a two-component signal transduction system (TCS), in addition to the enzymes for ethanolamine transport and catabolism. We show that the expression of most of these genes as well as BMC formation is highly increased in wild type fusobacteria when cultured in the presence of ethanolamine as a nutrient source. Deletion of the response regulator EutV eliminated this induction of eut mRNAs and BMCs, thus demonstrating that BMC formation is transcriptionally regulated by the TCS EutV-EutW in response to ethanolamine. Mass spectrometry of isolated BMCs unveiled the identity of the constituent proteins EutL, EutM1, EutM2, and EutN. Consistent with the role of these proteins in BMC assembly and metabolism, deletion of eutN, eutL/eutM1/eutM2, or eutL/eutM1/eutM2/eutN not only affected BMC formation, but also ethanolamine utilization, causing cell growth defects with ethanolamine as nutrient. BMCs also assembled in fusobacteria cultured with placental cells or the culture media, a process that is dependent on the BMC shell proteins. Significantly, we show that the eutN mutant is defective in inducing preterm birth in a mouse model. Together, these results establish that BMC-mediated metabolism of ethanolamine is critical for fusobacterial virulence. IMPORTANCEThe oral anaerobe Fusobacterium nucleatum can spread to distal internal organs, such as the colon and placenta, and thereby promote the development of colorectal cancer and induce preterm birth, respectively. Yet, how this opportunistic pathogen adapts to the various metabolically distinct host cellular niches remains poorly understood. We demonstrated here that this microbe assembles specialized metabolic organelles, termed bacterial microcompartments (BMCs), to utilize environmental ethanolamine (EA) as a key environmental nutrient source. The formation of F. nucleatum BMCs, containing BMC shell proteins EutLM1M2N, is controlled by a two-component system, EutV-EutW, responsive to EA. Significantly, this ability of F. nucleatum to form BMCs in response to EA is crucial for its pathogenicity evidenced by the fact that the genetic disruption of BMC formation reduces fusobacterial virulence in a mouse model of preterm birth.

microbiology↗

bioRxiv2024

Glutamine Transport via Neurotransmitter Transporter 4 (NTT4, SLC6A17) Maintains Presynaptic Glutamate Supply at Excitatory Synapses in the Central Nervous System

The glutamate-glutamine cycle is thought to be the principle metabolic pathway that recycles glutamate at excitatory synapses. In this cycle, synaptically released glutamate is sequestered by astrocytes and converted to glutamine before being returned to the presynaptic terminal for conversion back into glutamate to replenish the neurotransmitter pool. While many aspects of this cycle have been extensively studied, a key component remains unknown: the nature of the transporter responsible for the presynaptic uptake of glutamine. We hypothesise that neurotransmitter transporter 4 (NTT4/SLC6A17) plays this role. Accordingly, we generated NTT4 knockout mice to assess its contribution to presynaptic glutamine transport and synaptic glutamate supply. Using biochemical tracing of [1-13C] glucose and [1,2-13C] acetate in awake mice, we observe a reduction of neuronal glutamate supply when NTT4 is absent. In addition, direct electrical recording of hippocampal mossy fibre boutons reveals a presynaptic glutamine transport current that is entirely inhibited by genetic or pharmacological elimination of NTT4. The role of NTT4 in neurotransmission was demonstrated by electrophysiological recordings in acute hippocampal slices, which reveal that NTT4 is required to maintain vesicular glutamate content and to sustain adequate levels of glutamate supply during periods of high-frequency neuronal activity. Finally, behavioural studies in mice demonstrate a deficit in trace fear conditioning; a hippocampus-dependent memory paradigm, and abnormalities in nest building, anxiety behaviour, and social preference. These results demonstrate that NTT4 is a presynaptic glutamine transporter which is a central component of the glutamate-glutamine cycle. NTT4 and hence the glutamate-glutamine cycle maintain neuronal glutamate supply for excitatory neurotransmission during high-frequency synaptic activity, and are key regulators of memory retention and normal behaviour.

neuroscience↗

bioRxiv2024

Paused Polymerase synergises with transcription factors and RNA to enhance the transcriptional potential of promoters

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 (ER) binding is stabilized at Pol II-paused sites. This stabilization results from an increased dwell time of ER on chromatin, as revealed by single molecule tracking (SMT) experiments. Notably, short chromatin-associated RNAs generated by the paused Pol II contribute to enhancing ER binding at paused promoters. We also observe that pausing increases histone H3K27 acetylation (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 ER-mediated gene regulation.

molecular biology↗