The scales, mechanisms, and dynamics of the genome architecture
L Lizana, YB Schwartz - Science Advances, 2024 - science.org
Even when split into several chromosomes, DNA molecules that make up our genome are
too long to fit into the cell nuclei unless massively folded. Such folding must accommodate …
too long to fit into the cell nuclei unless massively folded. Such folding must accommodate …
Uncovering the principles of genome folding by 3D chromatin modeling
A Yildirim, L Boninsegna… - Cold Spring Harbor …, 2022 - cshperspectives.cshlp.org
Our understanding of how genomic DNA is tightly packed inside the nucleus, yet is still
accessible for vital cellular processes, has grown dramatically over recent years with …
accessible for vital cellular processes, has grown dramatically over recent years with …
Predicting chromatin architecture from models of polymer physics
S Bianco, AM Chiariello, C Annunziatella… - Chromosome …, 2017 - Springer
We review the picture of chromatin large-scale 3D organization emerging from the analysis
of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a …
of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a …
Structure of the human chromosome interaction network
New Hi-C technologies have revealed that chromosomes have a complex network of spatial
contacts in the cell nucleus of higher organisms, whose organisation is only partially …
contacts in the cell nucleus of higher organisms, whose organisation is only partially …
A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells
We investigate the three-dimensional (3D) conformations of the α-globin locus at the single-
allele level in murine embryonic stem cells (ESCs) and erythroid cells, combining polymer …
allele level in murine embryonic stem cells (ESCs) and erythroid cells, combining polymer …
Modeling single-molecule conformations of the HoxD region in mouse embryonic stem and cortical neuronal cells
Complex architectural rearrangements are associated to the control of the HoxD genes in
different cell types; yet, how they are implemented in single cells remains unknown. By use …
different cell types; yet, how they are implemented in single cells remains unknown. By use …
Polymer models for the mechanisms of chromatin 3D folding: review and perspective
R Zhou, YQ Gao - Physical Chemistry Chemical Physics, 2020 - pubs.rsc.org
Recent experiments have provided unprecedented details on the hierarchical organization
of the chromatin 3D structure and thus a great opportunity for understanding the …
of the chromatin 3D structure and thus a great opportunity for understanding the …
The interplay between phase separation and gene-enhancer communication: a theoretical study
AM Chiariello, F Corberi, M Salerno - Biophysical Journal, 2020 - cell.com
The phase separation occurring in a system of mutually interacting proteins that can bind on
specific sites of a chromatin fiber is investigated here. This is achieved by means of …
specific sites of a chromatin fiber is investigated here. This is achieved by means of …
Dynamic and equilibrium properties of finite-size polymer models of chromosome folding
M Conte, L Fiorillo, C Annunziatella, A Esposito… - Physical Review E, 2021 - APS
Novel technologies are revealing that chromosomes have a complex three-dimensional
organization within the cell nucleus that serves functional purposes. Models from polymer …
organization within the cell nucleus that serves functional purposes. Models from polymer …
Higher-order chromosome structures investigated by polymer physics in cellular morphogenesis and differentiation
Abstract Experimental advances in Molecular Biology demonstrated that chromatin
architecture and gene regulation are deeply related. Hi-C data, for instance, returned a …
architecture and gene regulation are deeply related. Hi-C data, for instance, returned a …