Katsuhiko Shirahige

The paper investigates how ESCO2-mediated acetylation of cohesin is distributed and retained across the genome, revealing region-specific patterns and post-replicative retention mechanisms.

This study shows cohesin regulates multiple transcription steps, with loss leading to reduced induction but minimal steady-state expression changes.

This study shows DNA catenation is essential for sister chromatid cohesion in budding yeast and metazoan chromosomes, as it provides force resistance necessary for accurate chromosome segregation.

This study shows that mutations in Asxl1 and Stag2 cause dysregulation of histone modifications and chromatin structures, leading to aberrant gene upregulation and myelodysplastic syndromes.

This study shows that Wpl1 and Eco1 regulate Scc2-cohesin interaction to limit DNA loop expansion and ensure proper mitotic chromosome segregation.

This study shows cohesin limits super elongation complex recruitment to promoters, thereby regulating RNA Polymerase II pausing and gene expression.

This study identifies Smc5/6's role in organizing transcription-induced positive DNA supercoils by initiating loop extrusion at cohesin-dependent boundaries.

The paper reveals an asymmetric response of DNA damage tolerance mechanisms to leading and lagging strand polymerase stalling.

This study shows that transcription and replication create chromosome loop boundaries by blocking cohesin progression, shaping S-phase chromosomes in yeast.

The paper identifies a new subset of cohesin binding sites, DICs, with distinct functions in transcriptional regulation across human cell types.

This study investigates how cohesin and related factors regulate 3D genome structure and gene expression by analyzing depletion effects on chromatin, transcriptome, and epigenome data.

The paper introduces a method to detect gene communities and identify mutually exclusive gene pairs from sparse scRNA-seq data, showing improved sensitivity in capturing cellular heterogeneity.

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

This study identifies age-dependent changes in rDNA copy number, methylation, and sequence variations in mice, linking these alterations to reduced pre-rRNA levels and shortened yeast lifespan.

This study shows Tex19.1 maintains acetylated SMC3 and sister chromatid cohesion in mouse oocytes, preventing aneuploidy.

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 uses CRISPR/Cas9 to generate NIPBL mutants and shows that the N-terminus of NIPBL is critical for transcriptional regulation by interacting with MAU2.

The paper introduces SSP, a tool to assess ChIP-seq data quality by measuring signal-to-noise ratio and peak reliability without peak calling, showing it is sensitive and robust across different factors and sequencing depths.

This study develops a yeast-based chemical-genetic screening system to annotate compound functionality across biological processes and identifies compounds with dual modes of action.