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 …

Decoding the organization, dynamics, and function of the 4D genome

E Aboelnour, B Bonev - Developmental Cell, 2021 - cell.com
Understanding how complex cell-fate decisions emerge at the molecular level is a key
challenge in developmental biology. Despite remarkable progress in decoding the …

3D or not 3D: shaping the genome during development

J Glaser, S Mundlos - Cold Spring Harbor Perspectives …, 2022 - cshperspectives.cshlp.org
One of the most fundamental questions in developmental biology is how one fertilized cell
can give rise to a fully mature organism and how gene regulation governs this process …

Understanding the 3D genome: emerging impacts on human disease

A Krumm, Z Duan - Seminars in cell & developmental biology, 2019 - Elsevier
Recent burst of new technologies that allow for quantitatively delineating chromatin structure
has greatly expanded our understanding of how the genome is organized in the three …

The second decade of 3C technologies: detailed insights into nuclear organization

A Denker, W De Laat - Genes & development, 2016 - genesdev.cshlp.org
The relevance of three-dimensional (3D) genome organization for transcriptional regulation
and thereby for cellular fate at large is now widely accepted. Our understanding of the …

The role of 3D genome organization in disease: from compartments to single nucleotides

A Chakraborty, F Ay - Seminars in cell & developmental biology, 2019 - Elsevier
Since the advent of the chromosome conformation capture technology, our understanding of
the human genome 3D organization has grown rapidly and we now know that human …

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 …

Organization and function of the 3D genome

B Bonev, G Cavalli - Nature Reviews Genetics, 2016 - nature.com
Understanding how chromatin is organized within the nucleus and how this 3D architecture
influences gene regulation, cell fate decisions and evolution are major questions in cell …

Gene regulation in the 3D genome

Y Li, M Hu, Y Shen - Human molecular genetics, 2018 - academic.oup.com
The spatial organization of the genome is essential for the precise control of gene
expression. Recent advances in sequencing and imaging technologies allow us to explore …

[HTML][HTML] The era of 3D and spatial genomics

BAM Bouwman, N Crosetto, M Bienko - Trends in genetics, 2022 - cell.com
Over a decade ago the advent of high-throughput chromosome conformation capture (Hi-C)
sparked a new era of 3D genomics. Since then the number of methods for mapping the 3D …