Hiroshi Kimurâ

The paper uses machine learning to classify chromatin classes and shows how different transcription systems affect nucleosome motion in distinct chromatin regions.

The paper investigates nuclear wrinkles in epithelial cells, finding they form due to geometric adaptations to mechanical stress and cell shape changes, without causing damage.

This paper identifies Ab-trapping as a staining artifact in antibody-based techniques, showing it results from high epitope abundance, high Ab affinity, and low diffusion rates, and suggests mitigation strategies.

The paper shows that chromatin modifications around genes fluctuate with transcriptional activity in mouse embryonic stem cells, revealing minute-scale coupling between histone marks and transcriptional bursts.

This paper presents an AI-driven method to convert antibody sequences into functional intrabodies, successfully converting 19 out of 26 sequences, including those targeting histone modifications.

The paper investigates how proximity of pre-mRNA 3' end processing and transcription termination affects gene expression in colorectal cancer, finding that closer proximity correlates with higher expression.

This study uses Nanoendoscopy-AFM to directly measure nuclear elasticity in cancer cells, finding increased elasticity under serum depletion and decreased elasticity with TGF-β treatment.

The paper identifies four types of fragile nucleosomes that facilitate RNA Polymerase II transcription in human cells by analyzing histone modifications and Pol II activity.

The paper identifies hypoacetylation-defined enhancers in luminal breast cancer cells and links them to subtype-specific gene regulation and patient classification.

The paper reconstructs artificial nuclei with nuclear import activity in living mouse oocytes using T4 phage DNA, showing they can form functional nuclear structures similar to natural nuclei.

This study shows that local DNA compaction forms TF-DNA clusters, which enable transcription by increasing TF binding sites and stabilizing the cluster.

This paper develops a genetically encoded probe to visualize H4K20me1 in living cells and demonstrates its utility in knock-in mice.

This study identifies three HP1 binding motifs in SUV420H2's HTM, showing that the second motif is critical for stabilizing HP1 on heterochromatin.

This study shows that NELF-C loss disrupts Pol II transcription termination and causes transcription-replication conflicts in colorectal cancer.

MAbID enables simultaneous profiling of multiple chromatin states in single cells, revealing multifactorial chromatin state changes during neural differentiation.

The paper uses live-cell imaging to show that H3K27ac and RNAP2-Ser5ph mark distinct chromatin sites with opposing nucleosome mobility dynamics.

The paper develops a STREAMING-tag system to study spatiotemporal relationships between transcriptional factors and activity in living cells.

This study identifies HULC and Set1C as factors that regulate heterochromatin organization during mating-type switching in fission yeast by controlling recombination enhancer usage and histone modifications.

This study shows that disrupting Smarce1 in mouse embryonic stem cells reduces nucleosome stability and impairs differentiation by altering chromatin structure.

This paper introduces EpiDamID, a method to profile histone modifications and transcriptomes at single-cell resolution, and demonstrates its application in mouse and zebrafish systems.

The paper introduces tsChIL, a method to analyze tissue-level epigenomic data from single-thin sections, enabling independent evaluation of cell population changes and gene activation in regenerating skeletal muscle.

This paper introduces TIP-seq, a high-throughput single-cell method for mapping DNA binding sites, achieving higher coverage and signal-to-noise than existing methods.

The paper uses live-cell imaging to study RNA polymerase II phosphorylation dynamics at a single gene, revealing spatial and temporal organization of phosphorylation clusters during transcription.

The paper introduces POINT technology to study co-transcriptional RNA processing, revealing insights into splicing kinetics, Xrn2 exonuclease specificity, and transcript termination mechanisms.

This study shows that oncogenic HRAS-induced senescence in human fibroblasts involves enhancer-promoter rewiring and dynamic cohesin binding, particularly at SASP genes.

The paper tracks H3K27me3 and H4K20me1 dynamics during XCI and finds they accumulate concurrently but have distinct genomic distributions, with H4K20me1 possibly contributing to chromatin compaction.

The paper shows that KDM7A and UTX demethylate repressive histone marks to enable NF-κB-dependent inflammatory gene activation in endothelial cells.

The paper characterizes the transcriptomic and epigenomic landscape of nine human endothelial cell types, identifying EC-specific enhancers and marker genes, and highlights the role of HOX genes in vascular development and disease.

This study investigates transcriptional bursting kinetics in mESCs using scRNA-seq and identifies regulatory factors and pathways influencing gene expression noise.

The paper investigates how JQ1 affects BRD2-dependent and independent transcription regulation without altering H4-hyperacetylated chromatin states in NSCLC cells.