4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modeling
Recent experimental observations suggest a strong coupling between the 3D nuclear
chromosome organization and epigenomics. However, the mechanistic and functional …
chromosome organization and epigenomics. However, the mechanistic and functional …
Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome
Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
functional processes, including transcription initiation, the pairwise motion of distal …
functional processes, including transcription initiation, the pairwise motion of distal …
Transcription processes compete with loop extrusion to homogenize promoter and enhancer dynamics
A Platania, C Erb, M Barbieri, B Molcrette… - Science …, 2024 - science.org
The spatiotemporal configuration of genes with distal regulatory elements is believed to be
crucial for transcriptional control, but full mechanistic understanding is lacking. We combine …
crucial for transcriptional control, but full mechanistic understanding is lacking. We combine …
Polymer folding through active processes recreates features of genome organization
From proteins to chromosomes, polymers fold into specific conformations that control their
biological function. Polymer folding has long been studied with equilibrium thermodynamics …
biological function. Polymer folding has long been studied with equilibrium thermodynamics …
In diverse conditions, intrinsic chromatin condensates have liquid-like material properties
Nuclear DNA in eukaryotes is wrapped around histone proteins to form nucleosomes on a
chromatin fiber. Dynamic folding of the chromatin fiber into loops and variations in the …
chromatin fiber. Dynamic folding of the chromatin fiber into loops and variations in the …
[HTML][HTML] Multiscale modeling of genome organization with maximum entropy optimization
ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …
role in all DNA-templated processes, including gene transcription, gene regulation, and …
Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization
Although our understanding of the involvement of heterochromatin architectural factors in
sha** nuclear organization is improving, there is still ongoing debate regarding the role of …
sha** nuclear organization is improving, there is still ongoing debate regarding the role of …
HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation
The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-
less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to …
less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to …
Crumpled polymer with loops recapitulates key features of chromosome organization
Chromosomes are exceedingly long topologically constrained polymers compacted in a cell
nucleus. We recently suggested that chromosomes are organized into loops by an active …
nucleus. We recently suggested that chromosomes are organized into loops by an active …