Biology subjects

Motamedi, M.

Publications and source records attributed to Motamedi, M..

7 recordsLinked to original sources

bioRxiv2025

Discrete Subdomains Establish Epigenetic Diversity in Subtelomeric Heterochromatin

Subtelomeres are imperfect repeats adjacent to telomeres that are transcriptionally repressed by heterochromatin. Although essential for genome integrity, their repetitive nature has thwarted dissection of local heterochromatin assembly and maintenance mechanisms. By engineering Schizosaccharomyces pombe strains carrying fluorescent reporters at a single subtelomere, we uncovered distinct subdomains. These subdomains have different silencing requirements: Telomere-proximal regions rely on canonical shelterin- or RNAi-dependent nucleation pathways, whereas telomere-distal regions involve nucleosome remodelers, histone chaperones, and boundary-associated factors. Subdomains also exhibit discrete epigenetic states emerging both at homologous loci on different chromosome arms and along the same subtelomeric sequence. We document these epigenetic states using multi-generational live imaging and targeted perturbations. These analyses show that subtelomeric subdomains display position-specific, clonally variable silencing across a spectrum from robust to fragile epigenetic states. Interestingly, structural variants, common in subtelomeric sequences across eukaryotes, dictate local epigenetic stability. These findings reveal that subtelomeres, long recognized for their sequence variability, form a dynamic mosaic of coexisting epigenetic domains. This implies a wide range of gene-repressive regulatory logic at the chromosome ends, from environmental responsiveness to silencing stability.

genomics↗

bioRxiv2025

Development of noninvasive imaging to measure spontaneous pain in mice

Objectively measuring pain in laboratory animals is essential for pain research and analgesic development. Despite the development of various behavioral tests to measure evoked pain in animal models, measuring spontaneous pain remains challenging. To address this unmet need, we developed a novel imaging approach to detect spontaneous nociception in animal pain models. To do this, we generated a Bacterial Artificial Chromosomes transgenic mouse that expresses Redquorin under the murine synapsin 1 promoter. Redquorin is a fusion protein consisting of chimera and a 2x tandem dimer Tomato Aequorin (tdTA), which emits long wavelength bioluminescence from activated neurons in the presence of coelenterazine. This luminescence can penetrate tissues and form a projected image on the body surface that can be detected with a spectrum In Vivo Imaging System, thus creating a Nociceptive Neuronal Activity Imaging mouse. We used the tdTA mice to image bioluminescence in the spinal regions as a surrogate of spontaneous pain induced by capsaicin, the HIV-1 envelope glycoprotein gp120, and spinal nerve ligation. Results show that Redquorin-emitted bioluminescence is a sensitive optical surrogate to measure spontaneous pain. This approach offers a new method to measure spontaneous pain in animal models for basic and translational research.

neuroscience↗

bioRxiv2025

Protocol for the development and use of spike-in control for chromatin immunoprecipitation (ChIP) of chromatin-binding proteins

Chromatin immunoprecipitation (ChIP) assays provide quantitative information about the genomic localization of chromatin-binding proteins. However, their sensitivity is limited by several technical variables. To generate high-confidence datasets, in this protocol, we used the Saccharomyces cerevisiae chromatin as an exogenous spike-in control for the ChIP of two S. pombe heterochromatin-associated proteins. This permitted normalization of the ChIP signals based on immunoprecipitation efficiencies across samples. Here, we describe the steps for spike-in control preparation, validation, and its use in data normalization. For complete details on the use and execution of this protocol, please refer to Khanduja et al.1

molecular biology↗

bioRxiv2022

Role of multiple pericentromeric repeats on heterochromatin assembly

Although the length and constituting sequences for pericentromeric repeats are highly variable across eukaryotes, the presence of multiple pericentromeric repeats is one of the conserved features of the eukaryotic chromosomes. Pericentromeric heterochromatin is often misregulated in human diseases, with the expansion of pericentromeric repeats in human solid cancers. In this article, we have developed a mathematical model of the RNAi-dependent methylation of H3K9 in the pericentromeric region of fission yeast. Our model, which takes copy number as an explicit parameter, predicts that the pericentromere is silenced only if there are many copies of repeats. It becomes bistable or desilenced if the copy number of repeats is reduced. This suggests that the copy number of pericentromeric repeats alone can determine the fate of heterochromatin silencing in fission yeast. Through sensitivity analysis, we identified parameters that favor bistability and desilencing. Stochastic simulation shows that faster cell division and noise favor the desilenced state. These results show the unexpected role of pericentromeric repeat copy number in gene silencing and elucidate how the copy number of silenced genomic regions may impact genome stability. Author SummaryPericentromeric repeats vary in length and sequences, but their presence is a conserved feature of eukaryotes. This suggests that the repetitive nature of pericentromeric sequences is an evolutionarily conserved feature of centromeres, which is under selective pressure. Here we developed a quantitative model for gene silencing at the fission yeast pericentromeric repeats. Our model is one of the first models which incorporates the copy number of pericentromeric repeats and predicts that the number of repeats can solely govern the dynamics of pericentromeric gene silencing. Our results suggest that the repeat copy number is a dynamic parameter for gene silencing, and copy-number-dependent silencing is an effective machinery to repress the repetitive part of the genome.

systems biology↗

bioRxiv2021

Hexavalent Sperm-Binding IgG Antibody Released from Self-Dissolving Vaginal Film Enables Potent, On-Demand Non-Hormonal Female Contraception

Non-hormonal products for on-demand contraception are a global health technology gap, motivating us to pursue the use of sperm-binding monoclonal antibodies as a strategy to enable safe, effective, desirable, on-demand contraception. Here, using cGMP-compliant Nicotiana-expression system, we produce an ultra-potent sperm-binding IgG antibody possessing 6 Fab arms per molecule that bind a well-established contraceptive antigen target, CD52g. We term this hexavalent antibody "Fab-IgG-Fab" (FIF) to reflect its molecular orientation. The Nicotiana-produced FIF exhibits at least 10-fold greater sperm agglutination potency and kinetics than the parent IgG, while preserving Fc-mediated trapping of individual spermatozoa in mucus. We formulate the Nicotiana-produced FIF into a polyvinyl alcohol-based water-soluble contraceptive film, and evaluate its potency in reducing progressively motile sperm in the sheep vagina. Two minutes after vaginal instillation of human semen, no progressively motile sperm are recovered from the vaginas of sheep receiving FIF-Film. In contrast, high numbers of progressively motile sperm are recovered from sheep receiving a placebo film control. Our work supports the potential of highly multivalent contraceptive antibodies to provide safe, effective, on-demand non-hormonal contraception.

bioengineering↗

bioRxiv2021

Gene clustering coordinates transcriptional output of disparate biological processes in eukaryotes

The establishment of distinct transcriptional states entails coordinated transcriptional coregulation of several disparate biological processes (BP), involving thousands of genes scattered throughout the genome. Linear clustering of genes in a single BP is one strategy for their transcriptional coregulation. However, whether such gene clustering also plays a role in transcriptional coherence of several disparate BPs remains unexplored. Here, by analyzing the genomes of eukaryotes ranging from yeast to human, we report the identification of thousands of conserved and species-specific disparate clustered BP pairs, many of which in normal human tissues are transcriptionally correlated. Strikingly, our results reveal that often this system-level transcriptional coordination is achieved in part by the genic proximity of regulatory nodes of disparate BPs whose coregulation drives the transcriptional coherence of their respective pathways. This, we hypothesize, is one strategy for creating coregulated, tunable modulons in eukaryotes.

systems biology↗

bioRxiv2018

Hydra Bcl-2 and TMBIMP family proteins display anti-apoptotic functions

BackgroundMechanisms of programmed cell death differ considerably between animals, plants and fungi. In animals they depend on caspases and Bcl-2 family proteins and this kind of cell death is called apoptosis. Most gene families encoding proteins involved in apoptosis are found in multicellular animals already in the eldest phyla but their functional conservation is still being studied. Much older protein families have cytoprotective functions across all kingdoms of life. This includes the TMBIMP-family, the presence and function of which in early metazoans has not been investigated yet.\n\nMethodsWe quantified apoptosis in transgenic Hydra overexpressing HyBcl-2-like 4. Moreover, we investigated putative TMBIMP-family members in Hydra by sequence comparison. By overexpression of TMBIMP-family members in Hydra and human HEK cells we analysed their subcellular localisation and in one case their capacity to protect cells from camptothecin induced apoptosis.\n\nResultsHyBcl-2-like 4, as previously shown in a heterologous system, was localised to mitochondria and able to protect Hydra epithelial cells from apoptosis. The TMBIMP-family in Hydra includes HyBax-Inhibitor-1, HyLifeguard-1a and -1b and HyLifeguard 4 proteins. HyBax-inhibitor-1 protein was found localised to ER-membranes, HyLifeguard-family members were found at the plasma membrane and in Golgi-vesicles. Moreover, HyBax-inhibitor-1 protected human cells from apoptosis.\n\nConclusionThis work provides the first functional study to support an anti-apoptotic function of Bcl-2 like proteins in pre-bilaterians within a physiological context. Furthermore it illustrates that genes that were \"inherited\" from non-animal ancestors, like the TMBIMP-family, were recruited to carry out cell protective anti-apoptotic functions already in early metazoans.

developmental biology↗