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 …

The role of chromosome domains in shaping the functional genome

T Sexton, G Cavalli - Cell, 2015 - cell.com
The genome must be highly compacted to fit within eukaryotic nuclei but must be accessible
to the transcriptional machinery to allow appropriate expression of genes in different cell …

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 …

Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq

Z Liu, Y Chen, Q Xia, M Liu, H Xu, Y Chi, Y Deng… - Science, 2023 - science.org
Much progress has been made recently in single-cell chromosome conformation capture
technologies. However, a method that allows simultaneous profiling of chromatin …

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 …

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 …

Epigenetic regulatory layers in the 3D nucleus

A Willemin, D Szabó, A Pombo - Molecular Cell, 2024 - cell.com
Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of
molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of …

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

I Williamson, S Berlivet, R Eskeland… - Genes & …, 2014 - genesdev.cshlp.org
Although important for gene regulation, most studies of genome organization use either
fluorescence in situ hybridization (FISH) or chromosome conformation capture (3C) …

The three-dimensional structure of human interphase chromosomes is related to the transcriptome map

S Goetze, J Mateos-Langerak, HJ Gierman… - … and cellular biology, 2007 - Taylor & Francis
The three-dimensional (3D) organization of the chromosomal fiber in the human interphase
nucleus is an important but poorly understood aspect of gene regulation. Here we …

Genomic interactions: chromatin loops and gene meeting points in transcriptional regulation

T Sexton, F Bantignies, G Cavalli - Seminars in cell & developmental …, 2009 - Elsevier
The chromosome conformation capture (3C) technique and its genome-wide applications
('4C') have identified a plethora of distal DNA sequences that are frequently in close spatial …