The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

SB Reiff, AJ Schroeder, K Kırlı, A Cosolo… - Nature …, 2022 - nature.com
Abstract The 4D Nucleome (4DN) Network aims to elucidate the complex structure and
organization of chromosomes in the nucleus and the impact of their disruption in disease …

Computational methods for analysing multiscale 3D genome organization

Y Zhang, L Boninsegna, M Yang, T Misteli… - Nature Reviews …, 2024 - nature.com
Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …

Functional organization of the human 4D Nucleome

H Chen, J Chen, LA Muir, S Ronquist… - Proceedings of the …, 2015 - National Acad Sciences
The 4D organization of the interphase nucleus, or the 4D Nucleome (4DN), reflects a
dynamical interaction between 3D genome structure and function and its relationship to …

[HTML][HTML] The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments

T Cremer, M Cremer, B Hübner, H Strickfaden… - FEBS letters, 2015 - Elsevier
Recent methodological advancements in microscopy and DNA sequencing-based methods
provide unprecedented new insights into the spatio-temporal relationships between …

Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations

L Boninsegna, A Yildirim, G Polles, Y Zhan… - Nature …, 2022 - nature.com
A multitude of sequencing-based and microscopy technologies provide the means to
unravel the relationship between the three-dimensional organization of genomes and key …

Structure and function in the nucleus

AI Lamond, WC Earnshaw - Science, 1998 - science.org
Current evidence suggests that the nucleus has a distinct substructure, albeit one that is
dynamic rather than a rigid framework. Viral infection, oncogene expression, and inherited …

Perspectives: using polymer modeling to understand the formation and function of nuclear compartments

N Haddad, D Jost, C Vaillant - Chromosome Research, 2017 - Springer
Compartmentalization is a ubiquitous feature of cellular function. In the nucleus, early
observations revealed a non-random spatial organization of the genome with a large-scale …

[HTML][HTML] 4D nucleome modeling

M Di Stefano, J Paulsen, D Jost… - Current opinion in …, 2021 - Elsevier
The intrinsic dynamic nature of chromosomes is emerging as a fundamental component in
regulating DNA transcription, replication, and damage-repair among other nuclear functions …

[HTML][HTML] Beyond the sequence: cellular organization of genome function

T Misteli - Cell, 2007 - cell.com
Genomes are more than linear sequences. In vivo they exist as elaborate physical
structures, and their functional properties are strongly determined by their cellular …

Genome modeling: from chromatin fibers to genes

S Portillo-Ledesma, Z Li, T Schlick - Current Opinion in Structural Biology, 2023 - Elsevier
The intricacies of the 3D hierarchical organization of the genome have been approached by
many creative modeling studies. The specific model/simulation technique combination …