Mechanics and functional consequences of nuclear deformations

Y Kalukula, AD Stephens, J Lammerding… - … reviews Molecular cell …, 2022 - nature.com
As the home of cellular genetic information, the nucleus has a critical role in determining cell
fate and function in response to various signals and stimuli. In addition to biochemical …

Exploring the contribution of ARMS2 and HTRA1 genetic risk factors in age-related macular degeneration

Y Pan, Y Fu, PN Baird, RH Guymer, T Das… - Progress in Retinal and …, 2023 - Elsevier
Age-related macular degeneration (AMD) is the leading cause of severe irreversible central
vision loss in individuals over 65 years old. Genome-wide association studies (GWASs) …

[HTML][HTML] Cell-type specialization is encoded by specific chromatin topologies

W Winick-Ng, A Kukalev, I Harabula, L Zea-Redondo… - Nature, 2021 - nature.com
Abstract The three-dimensional (3D) structure of chromatin is intrinsically associated with
gene regulation and cell function,–. Methods based on chromatin conformation capture have …

Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding

M Conte, E Irani, AM Chiariello, A Abraham… - Nature …, 2022 - nature.com
Loop-extrusion and phase-separation have been proposed as mechanisms that shape
chromosome spatial organization. It is unclear, however, how they perform relative to each …

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

RA Beagrie, CJ Thieme, C Annunziatella, C Baugher… - Nature …, 2023 - nature.com
Technology for measuring 3D genome topology is increasingly important for studying gene
regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and …

MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution

MV Neguembor, JP Arcon, D Buitrago… - Nature structural & …, 2022 - nature.com
The linear sequence of DNA provides invaluable information about genes and their
regulatory elements along chromosomes. However, to fully understand gene function and …

Function and evolution of the loop extrusion machinery in animals

E Kabirova, A Nurislamov, A Shadskiy… - International Journal of …, 2023 - mdpi.com
Structural maintenance of chromosomes (SMC) complexes are essential proteins found in
genomes of all cellular organisms. Essential functions of these proteins, such as mitotic …

Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser

D Li, JK Harrison, D Purushotham, T Wang - Nature Methods, 2022 - nature.com
To the Editor—Three-dimensional (3D) genomic structures are vital for gene regulation and
cell function1. High-throughput technologies based on chromosome conformation capture …

Network models of chromatin structure

V Pancaldi - Current Opinion in Genetics & Development, 2023 - Elsevier
Highlights•Networks are a useful framework to study chromatin structure
datasets.•Chromatin networks can be used to visualize the 3D epigenome and integrate …

Elucidating the structure and function of the nucleus—the NIH Common Fund 4D Nucleome program

AL Roy, RS Conroy, VG Taylor, J Mietz, IM Fingerman… - Molecular cell, 2023 - cell.com
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 …