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 …
function. Although 3D genome organization has been historically difficult to study owing to a …
Methods for mapping 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 …
understanding the role of chromatin topology in gene regulation. Several methods are …
Enhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion
Homotypic chromatin interactions and loop extrusion are thought to be the two main drivers
of mammalian chromosome folding. Here we tested the role of RNA polymerase II (RNAPII) …
of mammalian chromosome folding. Here we tested the role of RNA polymerase II (RNAPII) …
Formation of chromatin subcompartments by phase separation
Chromatin is partitioned on multiple length scales into subcompartments that differ from
each other with respect to their molecular composition and biological function. It is a key …
each other with respect to their molecular composition and biological function. It is a key …
Computational methods for analysing multiscale 3D genome organization
Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …
characterization of the spatial organization and folding of the genome in the nucleus. In …
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding
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 …
chromosome spatial organization. It is unclear, however, how they perform relative to each …
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains
The promoters of mammalian genes are commonly regulated by multiple distal enhancers,
which physically interact within discrete chromatin domains. How such domains form and …
which physically interact within discrete chromatin domains. How such domains form and …
Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation
The spatial organization of chromosomes has key functional roles, yet how chromosomes
fold remains poorly understood at the single-molecule level. Here, we employ models of …
fold remains poorly understood at the single-molecule level. Here, we employ models of …
Preformed chromatin topology assists transcriptional robustness of Shh during limb development
C Paliou, P Guckelberger, R Schöpflin… - Proceedings of the …, 2019 - National Acad Sciences
Long-range gene regulation involves physical proximity between enhancers and promoters
to generate precise patterns of gene expression in space and time. However, in some cases …
to generate precise patterns of gene expression in space and time. However, in some cases …
Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis
The regulatory specificity of enhancers and their interaction with gene promoters is thought
to be controlled by their sequence and the binding of transcription factors. By studying Pitx1 …
to be controlled by their sequence and the binding of transcription factors. By studying Pitx1 …