Naoki Kubo

HNRNPC-mediated RNA processing promotes VHL-associated excessive vasculogenesis in von Hippel-Lindau syndrome revealed from patient-derived blood vessel models

This study uses patient-derived iPSCs to model VHLS-associated excessive vasculogenesis and identifies HNRNPC as a key factor in VHL-driven vascular lesions independent of HIF2A.

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

The paper identifies 491,818 candidate cis regulatory elements in adult mouse brain sub-types and links them to target genes and transcriptional regulators involved in various pathways.

MUNIn (Multiple sample UNifying long-range chromatin Interaction detector): a statistical framework for identifying long-range chromatin interactions from multiple samples

MUNIn identifies long-range chromatin interactions across multiple samples by accounting for sequencing depth and heterogeneity, achieving lower false positives and higher power for shared peaks.

Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells

This study shows that chromatin organization remains largely intact in mouse embryonic stem cells after acute CTCF depletion, despite reduced cell growth and changes in chromatin loop interactions and cohesin occupancy.

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells

This study shows that CTCF depletion in mESCs weakens TAD boundaries and INs but only affects a small subset of enhancer-promoter contacts, highlighting CTCF's role in promoting long-range gene regulation.