Models of chromosome structure

M Nicodemi, A Pombo - Current opinion in cell biology, 2014 - Elsevier
Understanding the mechanisms that control chromosome folding in the nucleus of
eukaryotes and their contribution to gene regulation is a key open issue in molecular …

Genome-in-a-box: building a chromosome from the bottom up

A Birnie, C Dekker - ACS nano, 2020 - ACS Publications
Chromosome structure and dynamics are essential for life, as the way that our genomes are
spatially organized within cells is crucial for gene expression, differentiation, and genome …

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

M Barbieri, SQ **e, E Torlai Triglia… - Nature structural & …, 2017 - nature.com
Gene expression states influence the 3D conformation of the genome through poorly
understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a …

Structural modeling of chromatin integrates genome features and reveals chromosome folding principle

WJ **e, L Meng, S Liu, L Zhang, X Cai, YQ Gao - Scientific reports, 2017 - nature.com
How chromosomes fold into 3D structures and how genome functions are affected or even
controlled by their spatial organization remain challenging questions. Hi-C experiment has …

Structure of the human chromosome interaction network

S Sarnataro, AM Chiariello, A Esposito, A Prisco… - PLoS …, 2017 - journals.plos.org
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 …

Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity

X Capaldi, Z Liu, Y Zhang, L Zeng, R Reyes-Lamothe… - Soft matter, 2018 - pubs.rsc.org
Here we present a pneumatically-actuated nanofluidic platform that has the capability of
dynamically controlling the confinement environment of macromolecules in solution. Using a …

Molecular dynamics simulations of the strings and binders switch model of chromatin

C Annunziatella, AM Chiariello, A Esposito, S Bianco… - Methods, 2018 - Elsevier
In recent years interest has grown on the applications of polymer physics to model chromatin
folding in order to try to make sense of the complexity of experimental data emerging from …

Polymer models of the hierarchical folding of the Hox-B chromosomal locus

C Annunziatella, AM Chiariello, S Bianco, M Nicodemi - Physical Review E, 2016 - APS
As revealed by novel technologies, chromosomes in the nucleus of mammalian cells have a
complex spatial organization that serves vital functional purposes. Here we use models from …

A statistical model of intra-chromosome contact maps

LI Nazarov, MV Tamm, VA Avetisov, SK Nechaev - Soft matter, 2015 - pubs.rsc.org
A statistical model describing a fine structure of the intra-chromosome maps obtained by a
genome-wide chromosome conformation capture method (Hi–C) is proposed. The model …

Polymer models of the organization of chromosomes in the nucleus of cells

AM Chiariello, S Bianco, A Piccolo… - … Physics Letters B, 2015 - World Scientific
Understanding the mechanisms that control the organization of chromosomes in the space
of the nucleus of cells, and its contribution to gene regulation, is a key open issue in …