Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

J Dekker, MA Marti-Renom, LA Mirny - Nature Reviews Genetics, 2013 - nature.com
How DNA is organized in three dimensions inside the cell nucleus and how this affects the
ways in which cells access, read and interpret genetic information are among the longest …

Mechanisms of chromosome folding and nuclear organization: their interplay and open questions

L Mirny, J Dekker - Cold Spring Harbor perspectives in …, 2022 - cshperspectives.cshlp.org
Microscopy and genomic approaches provide detailed descriptions of the three-dimensional
folding of chromosomes and nuclear organization. The fundamental question is how activity …

[HTML][HTML] Formation of chromosomal domains by loop extrusion

G Fudenberg, M Imakaev, C Lu, A Goloborodko… - Cell reports, 2016 - cell.com
Topologically associating domains (TADs) are fundamental structural and functional
building blocks of human interphase chromosomes, yet the mechanisms of TAD formation …

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

I Miguel-Escalada, S Bonàs-Guarch, I Cebola… - Nature …, 2019 - nature.com
Genetic studies promise to provide insight into the molecular mechanisms underlying type 2
diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer …

CHiCAGO: robust detection of DNA loo** interactions in Capture Hi-C data

J Cairns, P Freire-Pritchett, SW Wingett, C Várnai… - Genome biology, 2016 - Springer
Abstract Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving
targeted regions of interest, such as gene promoters, globally and at high resolution. Signal …

Organization of the mitotic chromosome

N Naumova, M Imakaev, G Fudenberg, Y Zhan… - Science, 2013 - science.org
Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a
century their internal organization remains largely unsolved. We applied chromosome …

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

D Jost, P Carrivain, G Cavalli… - Nucleic acids research, 2014 - academic.oup.com
Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states.
These domains are stably inherited across many cell generations and can be remodeled in …

Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

DB Brückner, H Chen, L Barinov, B Zoller, T Gregor - Science, 2023 - science.org
Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
functional processes, including transcription initiation, the pairwise motion of distal …

From a melt of rings to chromosome territories: the role of topological constraints in genome folding

JD Halverson, J Smrek, K Kremer… - Reports on Progress in …, 2014 - iopscience.iop.org
We review pro and contra of the hypothesis that generic polymer properties of topological
constraints are behind many aspects of chromatin folding in eukaryotic cells. For that …

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics

JD Halverson, WB Lee, GS Grest… - The Journal of …, 2011 - pubs.aip.org
Molecular dynamics simulations were conducted to investigate the structural properties of
melts of nonconcatenated ring polymers and compared to melts of linear polymers. The …