Biology subjects

Kurotaki, D.

Publications and source records attributed to Kurotaki, D..

3 recordsLinked to original sources

bioRxiv2024

Dynamic and decay kinetics of H3 variants in live cells reveal the pivotal role of HIRA/NSD2 in maintaining the distinct H3.3 specific chromatin landscape

The incorporation of variant histone H3.3 into the genome is tightly linked with transcriptional activity, yet its precise regulatory mechanisms remain elusive. Traditional methods like Chromatin Immunoprecipitation offer static views of H3.3 distribution, lacking dynamic insights. Here, using the SNAP tag system, we employed Fluorescence Recovery After Photobleaching (FRAP) and live-cell imaging to investigate H3.3 mobility and decay kinetics in live mouse embryonic fibroblast cells. Our focus on interferon-induced transcriptional activation revealed rapid H3.3 exchange, indicative of its transcriptional regulatory role. Transcription inhibition hindered H3.3 mobility, emphasizing its involvement in transcription. Additionally, we probed into turnover dynamics(decay) of H3.1-SNAP and H3.3-SNAP variants, uncovering differential decay rates influenced by transcriptional activity and histone modifiers such as NSD2 and HIRA. Live-cell imaging showed faster decay of H3.3 compared to H3.1, further exacerbated upon NSD2/HIRA loss. Notably, HIRA and NSD2, regulators of H3.3 dynamics, proved crucial for both H3.3 mobility and decay, underscoring their pivotal role. These findings deepen our understanding of epigenetic regulation, emphasizing the dynamic nature of histone turnover in cellular function and its implications for disease pathogenesis. Taken together, this study sheds light on the dynamic behavior of H3.3 and its regulatory mechanisms, providing valuable insights into epigenetic regulation in cellular processes and disease contexts.

cell biology↗

bioRxiv2023

IRF8 configures enhancer landscape in postnatal microglia and directs microglia specific transcriptional programs

Microglia are innate immune cells in the brain. Transcription factor IRF8 is highly expressed in microglia. However, its role in postnatal microglia development is unknown. We demonstrate that IRF8 binds stepwise to enhancer regions of postnatal microglia along with Sall1 and PU.1, reaching a maximum after day 14. IRF8 binding correlated with a stepwise increase in chromatin accessibility, which preceded the initiation of microglia-specific transcriptome. Constitutive and postnatal Irf8 deletion led to a loss of microglia identity and gain of disease-associated microglia-like genes. Combined analysis of scRNA-seq and scATAC-seq revealed a correlation between chromatin accessibility and transcriptome at a single-cell level. IRF8 was also required for microglia-specific DNA methylation patterns. Lastly, in the 5xFAD model, constitutive and postnatal Irf8 deletion reduced the interaction of microglia with A{beta} plaques and the size of plaques, lessening neuronal loss. Together, IRF8 sets the epigenetic landscape, which is required for postnatal microglia gene expression.

immunology↗

bioRxiv2022

Inositol pyrophosphate profiling reveals regulatory roles of IP6K2-dependent enhanced IP7 metabolism in enteric nervous system

Inositol pyrophosphates (PP-IPs) regulate diverse physiological processes; to better understand their functional roles, assessing their tissue-specific distribution is important. Here, we profiled PP-IP levels in mammalian organs using a novel HILIC-MS/MS protocol and discovered that the gastrointestinal tract (GIT) contained the highest levels of IP7 and its precursor IP6. Although their absolute levels in the GIT is diet-dependent, elevated IP7 metabolism still exists under dietary regimes devoid of exogenous IP7. Of the major GIT cells, enteric neurons selectively express the IP7-synthesizing enzyme IP6K2. IP6K2-knockout mice exhibited significantly impaired IP7 metabolism in the various organs including the proximal GIT. Additionally, HILIC-MS/MS analysis displayed that genetic ablation of IP6K2 significantly impaired IP7 metabolism in the gut and duodenal muscularis externa containing myenteric plexus. Whole transcriptome analysis of duodenal muscularis externa further suggested that IP6K2 inhibition induced the gene sets associated with mature neurons such as inhibitory, GABAergic and dopaminergic neurons, concomitantly with suppression of those for neural progenitor/stem cells and glial cells. In addition, IP6K2 inhibition explicitly affected transcript levels of certain genes modulating neuronal differentiation and functioning, implying critical roles of IP6K2-IP7 axis in developmental and functional regulation of enteric nervous system. These results collectively reveal an unexpected role of mammalian IP7--a highly active IP6K2-IP7 pathway is conducive to enteric nervous system.

molecular biology↗