PRC2, chromatin regulation, and human disease: insights from molecular structure and function
X Liu, X Liu - Frontiers in Oncology, 2022 - frontiersin.org
Polycomb repressive complex 2 (PRC2) is a multisubunit histone-modifying enzyme
complex that mediates methylation of histone H3 lysine 27 (H3K27). Trimethylated H3K27 …
complex that mediates methylation of histone H3 lysine 27 (H3K27). Trimethylated H3K27 …
Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks
Implicit solvent models are essential for molecular dynamics simulations of biomolecules,
striking a balance between computational efficiency and biological realism. Efforts are …
striking a balance between computational efficiency and biological realism. Efforts are …
Explicit ion modeling predicts physicochemical interactions for chromatin organization
Molecular mechanisms that dictate chromatin organization in vivo are under active
investigation, and the extent to which intrinsic interactions contribute to this process remains …
investigation, and the extent to which intrinsic interactions contribute to this process remains …
Dynamical phase transition in models that couple chromatin folding with histone modifications
Genomic regions can acquire heritable epigenetic states through unique histone
modifications, which lead to stable gene expression patterns without altering the underlying …
modifications, which lead to stable gene expression patterns without altering the underlying …
On the stability and layered organization of protein-DNA condensates
Multi-component phase separation is emerging as a key mechanism for the formation of
biological condensates that play essential roles in signal sensing and transcriptional …
biological condensates that play essential roles in signal sensing and transcriptional …
Chromatin fiber breaks into clutches under tension and crowding
The arrangement of nucleosomes inside chromatin is of extensive interest. While in vitro
experiments have revealed the formation of 30 nm fibers, most in vivo studies have failed to …
experiments have revealed the formation of 30 nm fibers, most in vivo studies have failed to …
Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction
Genome-wide chromosome conformation capture (Hi-C) experiments have revealed many
structural features of chromatin across multiple length scales. Further understanding …
structural features of chromatin across multiple length scales. Further understanding …
OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates
Biomolecular condensates are important structures in various cellular processes but are
challenging to study using traditional experimental techniques. In silico simulations with …
challenging to study using traditional experimental techniques. In silico simulations with …
Phase separation and correlated motions in motorized genome
The human genome is arranged in the cell nucleus nonrandomly, and phase separation has
been proposed as an important driving force for genome organization. However, the cell …
been proposed as an important driving force for genome organization. However, the cell …
Coupling chromatin folding with histone modifications reveals dynamical asymmetry in the epigenetic landscape
Genomic regions adopt heritable epigenetic states with unique histone modifications,
resulting in bistable gene expression without changes to the underlying DNA sequence. The …
resulting in bistable gene expression without changes to the underlying DNA sequence. The …