[HTML][HTML] Polymer physics of chromosome large-scale 3D organisation
… Here we show that genome-wide chromatin architecture data, as mapped by Hi-C methods
across mammalian cell types and chromosomes, are well described by classical scaling …
across mammalian cell types and chromosomes, are well described by classical scaling …
Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis
…, V Heinrich, R Schöpflin, A Esposito, C Annunziatella… - Nature …, 2018 - nature.com
… First, we compared Capture-C interaction tracks from the … c, The subtraction of WT and Pitx1
delL/delL CHi-C from … Capture-C profiles using Pitx1 as a viewpoint derived from CHi-C in …
delL/delL CHi-C from … Capture-C profiles using Pitx1 as a viewpoint derived from CHi-C in …
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 complex …
of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex …
Polymer physics predicts the effects of structural variants on chromatin architecture
…, DG Lupiáñez, AM Chiariello, C Annunziatella… - Nature …, 2018 - nature.com
… In the studied murine Epha4 locus, the algorithm returns n* = 21 and λ* = 1.0 in both the
published in situ Hi-C data of CH12-LX cells 23 and in our limb tissue cHi-C data. In the …
published in situ Hi-C data of CH12-LX cells 23 and in our limb tissue cHi-C data. In the …
Preformed chromatin topology assists transcriptional robustness of Shh during limb development
…, S Bianco, C Annunziatella… - Proceedings of the …, 2019 - National Acad Sciences
… (C) Virtual capture-C (vC) profiles using Shh promoter as viewpoint derived from cHi-C in
E10.… (D) A 3D polymer model of wildtype and ΔCTCF i4:i5 limb cHi-C data. Note the changes in …
E10.… (D) A 3D polymer model of wildtype and ΔCTCF i4:i5 limb cHi-C data. Note the changes in …
[HTML][HTML] Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
RA Beagrie, CJ Thieme, C Annunziatella, C Baugher… - Nature …, 2023 - nature.com
Technology for measuring 3D genome topology is increasingly important for studying gene
regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and …
regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and …
Molecular dynamics simulations of the strings and binders switch model of chromatin
… 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 new technologies such as Hi-C or …
sense of the complexity of experimental data emerging from new technologies such as Hi-C or …
[PDF][PDF] A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells
… Next, to support our results based on Capture-C data and to investigate the structural … inferred
from Capture-C data correspond to the three key binding sites of the toy model (Figure 5C). …
from Capture-C data correspond to the three key binding sites of the toy model (Figure 5C). …
Models of polymer physics for the architecture of the cell nucleus
A Esposito, C Annunziatella, S Bianco… - … Systems Biology and …, 2019 - Wiley Online Library
The depth and complexity of data now available on chromosome 3D architecture, derived
by new technologies such as Hi‐C, have triggered the development of models based on …
by new technologies such as Hi‐C, have triggered the development of models based on …
[PDF][PDF] Modeling single-molecule conformations of the HoxD region in mouse embryonic stem and cortical neuronal cells
… That information is unavailable in usual Hi-C data but can be easily extracted with our models.
The formation of strips of enhanced interaction between the region of duplication and the …
The formation of strips of enhanced interaction between the region of duplication and the …