Challenges and guidelines toward 4D nucleome data and model standards
MA Marti-Renom, G Almouzni, WA Bickmore… - Nature …, 2018 - nature.com
Due to recent advances in experimental and theoretical approaches, the dynamic three-
dimensional organization (3D) of the nucleus has become a very active area of research in …
dimensional organization (3D) of the nucleus has become a very active area of research in …
Elucidating the structure and function of the nucleus—the NIH Common Fund 4D Nucleome program
Genomic architecture appears to play crucial roles in health and a variety of diseases. How
nuclear structures reorganize over different timescales is elusive, partly because the tools …
nuclear structures reorganize over different timescales is elusive, partly because the tools …
[HTML][HTML] Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome
and the nucleus in space and time. We summarize progress by the consortium and highlight …
and the nucleus in space and time. We summarize progress by the consortium and highlight …
The 4D nucleome project
Abstract The 4D Nucleome Network aims to develop and apply approaches to map the
structure and dynamics of the human and mouse genomes in space and time with the goal …
structure and dynamics of the human and mouse genomes in space and time with the goal …
[HTML][HTML] 4D nucleome modeling
The intrinsic dynamic nature of chromosomes is emerging as a fundamental component in
regulating DNA transcription, replication, and damage-repair among other nuclear functions …
regulating DNA transcription, replication, and damage-repair among other nuclear functions …
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 …
4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?
Genome-wide sequencing technologies enable investigations of the structural properties of
the genome in various spatial dimensions. Here, we review computational techniques …
the genome in various spatial dimensions. Here, we review computational techniques …
In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization
E Oberbeckmann, K Quililan, P Cramer… - Nature Genetics, 2024 - nature.com
Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms
driving the formation of these domains are difficult to dissect in vivo and remain poorly …
driving the formation of these domains are difficult to dissect in vivo and remain poorly …
Unraveling the 3D genome: genomics tools for multiscale exploration
VI Risca, WJ Greenleaf - Trends in Genetics, 2015 - cell.com
A decade of rapid method development has begun to yield exciting insights into the 3D
architecture of the metazoan genome and the roles it may play in regulating transcription …
architecture of the metazoan genome and the roles it may play in regulating transcription …
3D genome architecture from populations to single cells
M Furlan-Magaril, C Varnai, T Nagano… - Current opinion in genetics …, 2015 - Elsevier
Dominated by microscopy for decades the nuclear genome organization field has recently
undergone a dramatic transition fuelled by new next generation sequencing technologies …
undergone a dramatic transition fuelled by new next generation sequencing technologies …