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 …

[HTML][HTML] Chromosome conformation capture and beyond: toward an integrative view of chromosome structure and function

RP McCord, N Kaplan, L Giorgetti - Molecular cell, 2020 - cell.com
Rapidly develo** technologies have recently fueled an exciting era of discovery in the
field of chromosome structure and nuclear organization. In addition to chromosome …

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

SM Espinola, M Götz, M Bellec, O Messina, JB Fiche… - Nature …, 2021 - nature.com
Acquisition of cell fate is thought to rely on the specific interaction of remote cis-regulatory
modules (CRMs), for example, enhancers and target promoters. However, the precise …

Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins

VS Lioy, A Cournac, M Marbouty, S Duigou… - Cell, 2018 - cell.com
As in eukaryotes, bacterial genomes are not randomly folded. Bacterial genetic information
is generally carried on a circular chromosome with a single origin of replication from which …

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

F Serra, D Baù, M Goodstadt, D Castillo… - PLoS computational …, 2017 - journals.plos.org
The sequence of a genome is insufficient to understand all genomic processes carried out in
the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is …

[HTML][HTML] Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions

Y Zhao, C Coelho, AL Hughes, L Lazar-Stefanita… - Cell, 2023 - cell.com
The Sc2. 0 project is building a eukaryotic synthetic genome from scratch. A major milestone
has been achieved with all individual Sc2. 0 chromosomes assembled. Here, we describe …

[HTML][HTML] Design, construction, and functional characterization of a tRNA neochromosome in yeast

D Schindler, RSK Walker, S Jiang, AN Brooks, Y Wang… - Cell, 2023 - cell.com
Here, we report the design, construction, and characterization of a tRNA neochromosome, a
designer chromosome that functions as an additional, de novo counterpart to the native …

Polymer physics predicts the effects of structural variants on chromatin architecture

S Bianco, DG Lupiáñez, AM Chiariello… - Nature …, 2018 - nature.com
Structural variants (SVs) can result in changes in gene expression due to abnormal
chromatin folding and cause disease. However, the prediction of such effects remains a …

Condensin-and replication-mediated bacterial chromosome folding and origin condensation revealed by Hi-C and super-resolution imaging

M Marbouty, A Le Gall, DI Cattoni, A Cournac, A Koh… - Molecular cell, 2015 - cell.com
Chromosomes of a broad range of species, from bacteria to mammals, are structured by
large topological domains whose precise functional roles and regulatory mechanisms …

Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes

A Bignaud, C Cockram, C Borde, J Groseille… - Nature Structural & …, 2024 - nature.com
Transcription generates local topological and mechanical constraints on the DNA fiber,
leading to the generation of supercoiled chromosome domains in bacteria. However, the …