Biology subjects

Lee, M.-K.

Publications and source records attributed to Lee, M.-K..

8 recordsLinked to original sources

bioRxiv2026

Temporal degradation of PRC2 uncovers specific developmental dependencies

The repression of genes by Polycomb repressive complex 2 (PRC2) is well documented and constitutive deletion studies have highlighted its essential role in development. However, exactly how loss of the complex is linked to these phenotypes remains incompletely understood and difficult to study in vivo. Here, we applied a rapid protein degradation strategy combined with a scalable embryoid model to trigger temporal PRC2 loss. This allowed us to fine-map developmental failures and showed that in addition to the canonical posterior phenotypes, PRC2-depleted embryoids display unexpected ectopic expression of anterior and lateral lineage genes. We also find that while the baseline enrichment of H3K27me3 generally predicts lineage sensitivity, the presence of cognate transcription factors ultimately helps explain which genes respond to PRC2 loss. Our integrative expression and chromatin profiling highlights that in contrast to developmental genes, pluripotency-associated genes only fail to silence with early PRC2 depletion but are unaffected once cells exited pluripotency. Together, our results shed new light on the specific developmental requirements for PRC2-mediated repression at unprecedented temporal and lineage resolution.

developmental biology↗

bioRxiv2026

Endogenous nucleophilic scavengers of reactive acyl-species neutralize carbon stress

Aberrant protein acylation by reactive acyl species (RAS)--termed carbon stress--is a major driver of aging and metabolic disease. While enzymatic deacylases such as sirtuins counteract aberrant acylation, whether endogenous metabolites can directly neutralize RAS remains unclear. Here, we report that nucleophilic metabolites--taurine, spermidine, and ethanolamine--react with acyl-CoAs, preventing aberrant protein acylation and potentially extending lifespan. We demonstrate that spermidine scavenges acetyl-CoA within the catalytic pocket of p300, a histone acetyltransferase, and extends lifespan in Drosophila. Taurine supplementation in mice fed a high-fat diet promotes N-fatty acyl taurine formation, confirming in vivo scavenging of RAS. These findings identify endogenous nucleophilic metabolites as scavengers that neutralize carbon stress, with implications for combating aging and metabolic disease. SummaryProtein homeostasis is constantly challenged by reactive metabolic intermediates that drive aberrant post-translational modifications, contributing to aging and metabolic disease. While the antioxidant systems that neutralize reactive oxygen species (ROS) are well characterized, whether analogous defenses exist against reactive acyl species (RAS)--the metabolic drivers of non-enzymatic protein acylation, termed carbon stress--has remained unknown. Here we show that three abundant endogenous nucleophilic metabolites--taurine, spermidine, and ethanolamine--directly intercept reactive acyl-CoA species through nucleophilic attack, preventing aberrant protein acylation. We demonstrate that spermidine scavenges acetyl-CoA within the catalytic pocket of the histone acetyltransferase p300, effectively buffering p300-mediated hyperacetylation of muscle, cytosolic, and mitochondrial proteins and extending lifespan in a Drosophila model of p300-driven toxicity. In mice fed a high-fat diet, taurine supplementation promotes the formation of N-fatty acyl taurines, providing direct in vivo evidence for nucleophilic scavenging of diet-derived RAS. Our findings reveal a previously unrecognized metabolite-based defense system--parallel to classical antioxidant defenses against ROS--that neutralizes carbon stress, with broad implications for understanding the molecular mechanisms of aging and the long-observed but mechanistically unexplained health benefits of taurine and spermidine.

biochemistry↗

bioRxiv2025

Local optogenetic control of genome editing and tumorigenesis in vivo using wireless implantable optoelectronics

Precise spatial regulation of site-specific DNA recombination (SSR) in vivo remains a challenge due to limited tunability of current platforms. Here, we present an optogenetic approach that overcome these limitations by employing engineered light-regulated recombinase E-LightR-Cre and tunable wireless implantable optoelectronic devices. E-LightR-Cre meets the key criteria for spatial regulation of SSR in vivo, showing no detectable activity in the dark, while demonstrating robust activation upon blue-light illumination. To achieve local E-LightR-Cre activation in murine lungs, we developed wireless, fully-implantable optoelectronic devices enabling focal illumination with no discernible organ damage. By modulating illumination intensity and duration, we can control the size of the activated area. Local expression of oncogenic KRas-G12D in a photoactivated subpopulation of cells in vitro revealed rapid reprogramming of the mutant expressing cells and their non-activated neighbors. Light-guided activation of E-LightR-Cre in mouse lungs resulted in focal expression of a reporter gene and allowed us to induce local formation of oncogenic lesions in vivo.

bioengineering↗

bioRxiv2024

An integrated microfluidic and fluorescence platform for probing in vivo neuropharmacology

Neurotechnologies and genetic tools for dissecting neural circuit functions have advanced rapidly over the past decade, although the development of complementary pharmacological method-ologies has comparatively lagged. Understanding the precise pharmacological mechanisms of neuroactive compounds is critical for advancing basic neurobiology and neuropharmacology, as well as for developing more effective treatments for neurological and neuropsychiatric disorders. However, integrating modern tools for assessing neural activity in large-scale neural networks with spatially localized drug delivery remains a major challenge. Here, we present a dual microfluidic-photometry platform that enables simultaneous intracranial drug delivery with neural dynamics monitoring in the rodent brain. The integrated platform combines a wireless, battery-free, miniaturized fluidic microsystem with optical probes, allowing for spatially and temporally specific drug delivery while recording activity-dependent fluorescence using genetically encoded calcium indicators (GECIs), neurotransmitter sensors GRABNE and GRABDA, and neuropeptide sensors. We demonstrate the performance this platform for investigating neuropharmacological mechanisms in vivo and characterize its efficacy in probing precise mechanistic actions of neuroactive compounds across several rapidly evolving neuroscience domains.

neuroscience↗

bioRxiv2023

Comparison of New and Old BacT/Alert Aerobic Bottles for Detection of Candida spp.

PurposeA new version of aerobic blood culture media has been developed for the BacT/Alert (bioMerieux) blood culture system. We evaluated the TTD and yeast cell counts in positive blood cultures for each Candida spp. according to changes in media. MethodsIsolates from defibrinated horse blood were inoculated into three types of bottles: the old version of FA Plus (Old FA Plus), New FA Plus, and FN Plus. All bottles were incubated in the BacT/Alert Virtuo blood culture system. The TTD was monitored for each bottle, and yeast cell counts were performed immediately after testing positive, determined via the plate count method. Clinical retrospective data of the candidemia samples before and after aerobic bottle change also were analyzed. ResultsThe mean TTD was 51.2 hours in the Old FA Plus bottles versus 19.5 hours in the New FA Plus bottles (P < 0.001) for Candida glabrata, and standard and clinical strains showed similar results. C. albicans (27.6 to 25.1 hours) and C. guilliermondii (28.8 to 27.3 hours) had shorter TTDs. However, C. auris (25.6 to 28.1 hours) had a longer TTD in the New FA Plus bottle. The retrospective clinical analysis showed a significant decrease in TTD (45.0 to 19.4 hours) for C. glabrata, which is consistent with our simulated study. ConclusionThis study shows that the TTD of C. glabrata was markedly reduced in the New FA Plus bottle due to the optimized growth performance. The reduction of TTD enables faster detection and therapeutic approach for C. glabrata infections.

microbiology↗

bioRxiv2020

Transcriptomic, protein-DNA interaction, and metabolomic studies of VosA, VelB, and WetA in Aspergillus nidulans asexual spores

In filamentous fungi, asexual development involves morphological differentiation and metabolic changes leading to the formation of asexual spores. The process of asexual spore formation in Aspergillus is precisely regulated by multiple transcription factors (TFs), including VosA, VelB, and WetA, and these three TFs are key regulators of the formation and maturation of asexual spores (conidia) in Aspergillus including the model fungus Aspergillus nidulans. To gain a mechanistic insight on the complex regulatory roles of these TFs in asexual spores, we conducted genome-wide studies on the expression, protein-DNA interactions, and primary and secondary metabolism employing A. nidulans conidia. RNA sequencing and chromatin immunoprecipitation-sequencing data have revealed that the three TFs directly or indirectly regulate the expression of genes associated with spore-wall formation/integrity, asexual development, and secondary metabolism. In addition, metabolomics analyses of wild-type and mutant conidia indicate that these three TFs regulate a diverse array of primary and secondary metabolism. In summary, WetA, VosA, and VelB play inter-dependent and distinct roles governing morphological development and primary/secondary metabolic remodeling in Aspergillus conidia. ImportanceFilamentous fungi produce a vast number of asexual spores that act as reproductive and propagator cells. These spores affect humans, due to the infectious or allergenic nature of the propagule. Aspergillus species produce asexual spores called conidia and their formation involves morphological development and metabolic changes, and the associated regulatory systems are coordinated by spore-specific transcription factors. To understand the underlying global regulatory programs and cellular outcomes associated with conidia formation, functional genomic and metabolomic analyses were performed in the model fungus Aspergillus nidulans. Our results show that the fungus specific WetA/VosA/VelB transcription factors govern the coordination of morphological and chemical developments during sporogenesis. The results of this study provide insights into the genetic regulatory networks about how morphological developments and metabolic changes are coordinated in fungi. The findings are relevant for other Aspergillus species such as the major human pathogen Aspergillus fumigatus and the aflatoxin-producer Aspergillus flavus.

microbiology↗

bioRxiv2018

Conservation and Divergence in the Asexual Sporulation Gene Regulatory Network Across a Genus of Filamentous Fungi

Asexual sporulation is fundamental to the ecology and lifestyle of filamentous fungi and can facilitate both plant and human infection. In Aspergillus, the production of asexual spores is primarily governed by the BrlA[->]AbaA[->]WetA regulatory cascade. The final step in this cascade is controlled by the WetA protein and not only governs the morphological differentiation of spores but also the production and deposition of diverse metabolites into spores. While WetA is conserved across the genus Aspergillus, the structure and degree of conservation of the wetA gene regulatory network (GRN) remains largely unknown. We carried out comparative transcriptome analyses between wetA null mutant and wild type asexual spores in three representative species spanning the diversity of the genus Aspergillus: A. nidulans, A. flavus, and A. fumigatus. We discovered that WetA regulates asexual sporulation in all three species via a negative feedback loop that represses BrlA, the cascades first step. Furthermore, ChIP-seq experiments in A. nidulans asexual spores suggest that WetA is a DNA-binding protein that interacts with a novel regulatory motif. Several global regulators known to bridge spore production and the production of secondary metabolites show species-specific regulatory patterns in our data. These results suggest that the BrlA[->]AbaA[->]WetA cascades regulatory role in cellular and chemical asexual spore development is functionally conserved, but that the wetA-associated GRN has diverged during Aspergillus evolution.

microbiology↗

bioRxiv2018

The BAP1 deubiquitinase complex is a general transcriptional co-activator

In Drosophila, a complex consisting of Calypso and ASX catalyzes H2A deubiquitination and has been reported to act as part of the Polycomb machinery in transcriptional silencing. The mammalian homologs of these proteins (BAP1 and ASXL1/2/3, respectively), are frequently mutated in various cancer types, yet their precise functions remain unclear. Using an integrative approach based on isogenic cell lines generated with CRISPR/Cas9, we uncover an unanticipated role for BAP1 in gene activation. This function requires the assembly of an enzymatically active BAPl-associated core complex (BAP1.com) containing one of the redundant ASXL proteins. We investigated the mechanism underlying BAP1.com-mediated transcriptional regulation and show that it functions neither in synergy nor by antagonism with the Polycomb machinery. Instead, our results provide compelling evidence that BAP1.com acts as a general transcriptional co-activator.

genomics↗