Ruyi Gong

Gene transcription and chromatin packing domains form a self-organizing system

The paper shows that Pol-II regulates chromatin packing domains through transcriptional loops, linking RNA synthesis to genome organization and gene expression.

Geometrically encoded positioning of introns, intergenic segments, and exons in the human genome

The paper proposes that introns, intergenic segments, and exons are positioned geometrically within chromatin domains to sustain transcriptional memory and reconcile epigenetic patterns and mutation non-randomness.

Leveraging chromatin packing domains to target chemoevasion in vivo

This study develops a physics-based model linking chromatin organization to chemoevasion, identifies TPR compounds that enhance chemotherapy efficacy in ovarian cancer.

Three-color single-molecule localization microscopy in chromatin

This paper develops a three-color single-molecule localization microscopy protocol to study chromatin structure, revealing that heterochromatin and euchromatin are not distinct territories but are spatially coupled.

Nuclear blebs are associated with destabilized chromatin packing domains

The paper investigates how nuclear blebs alter chromatin packing domains, finding fragmentation of nanoscopic heterochromatin domains within blebs.

mRNA expression is co-regulated by non-nucleolar RNA polymerase I

The paper shows that RNA polymerase I co-regulates chromatin domains and mRNA synthesis with RNA polymerase II, affecting genome connectivity and gene expression.