Understanding 3D genome organization by multidisciplinary methods

I Jerkovic, G Cavalli - Nature reviews Molecular cell biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

J Dekker, F Alber, S Aufmkolk, BJ Beliveau… - Molecular cell, 2023 - cell.com
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 …

3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

CM Uyehara, E Apostolou - Cell reports, 2023 - cell.com
The spatiotemporal control of gene expression is dependent on the activity of cis-acting
regulatory sequences, called enhancers, which regulate target genes over variable genomic …

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 map** and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …

Methods for map** 3D chromosome architecture

R Kempfer, A Pombo - Nature Reviews Genetics, 2020 - nature.com
Determining how chromosomes are positioned and folded within the nucleus is critical to
understanding the role of chromatin topology in gene regulation. Several methods are …

Clinical application of advanced multi-omics tumor profiling: Sha** precision oncology of the future

D Akhoundova, MA Rubin - Cancer Cell, 2022 - cell.com
Next-generation DNA sequencing technology has dramatically advanced clinical oncology
through the identification of therapeutic targets and molecular biomarkers, leading to the …

Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

AS Deshpande, N Ulahannan, M Pendleton… - Nature …, 2022 - nature.com
Abstract High-order three-dimensional (3D) interactions between more than two genomic
loci are common in human chromatin, but their role in gene regulation is unclear. Previous …

Resolving the 3D landscape of transcription-linked mammalian chromatin folding

THS Hsieh, C Cattoglio, E Slobodyanyuk, AS Hansen… - Molecular cell, 2020 - cell.com
Whereas folding of genomes at the large scale of epigenomic compartments and
topologically associating domains (TADs) is now relatively well understood, how chromatin …

Current challenges in understanding the role of enhancers in disease

JB Zaugg, P Sahlén, R Andersson… - Nature structural & …, 2022 - nature.com
Enhancers play a central role in the spatiotemporal control of gene expression and tend to
work in a cell-type-specific manner. In addition, they are suggested to be major contributors …

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 …