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 …

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 …

Complex multi-enhancer contacts captured by genome architecture mapping

RA Beagrie, A Scialdone, M Schueler, DCA Kraemer… - Nature, 2017 - nature.com
The organization of the genome in the nucleus and the interactions of genes with their
regulatory elements are key features of transcriptional control and their disruption can cause …

Three-dimensional genome architecture: players and mechanisms

A Pombo, N Dillon - Nature reviews Molecular cell biology, 2015 - nature.com
The different cell types of an organism share the same DNA, but during cell differentiation
their genomes undergo diverse structural and organizational changes that affect gene …

[HTML][HTML] Allostery in disease and in drug discovery

R Nussinov, CJ Tsai - Cell, 2013 - cell.com
Allostery is largely associated with conformational and functional transitions in individual
proteins. This concept can be extended to consider the impact of conformational …

A decade of 3C technologies: insights into nuclear organization

E De Wit, W De Laat - Genes & development, 2012 - genesdev.cshlp.org
Over the past 10 years, the development of chromosome conformation capture (3C)
technology and the subsequent genomic variants thereof have enabled the analysis of …

Nuclear compartments: an incomplete primer to nuclear compartments, bodies, and genome organization relative to nuclear architecture

AS Belmont - Cold Spring Harbor perspectives in biology, 2022 - cshperspectives.cshlp.org
This work reviews nuclear compartments, defined broadly to include distinct nuclear
structures, bodies, and chromosome domains. It first summarizes original cytological …

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

B Lenhard, A Sandelin, P Carninci - Nature Reviews Genetics, 2012 - nature.com
Promoters are crucial for gene regulation. They vary greatly in terms of associated regulatory
elements, sequence motifs, the choice of transcription start sites and other features. Several …

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs

E Brookes, I de Santiago, D Hebenstreit, KJ Morris… - Cell stem cell, 2012 - cell.com
Polycomb repressor complexes (PRCs) are important chromatin modifiers fundamentally
implicated in pluripotency and cancer. Polycomb silencing in embryonic stem cells (ESCs) …

RNA polymerase II clusters form in line with surface condensation on regulatory chromatin

A Pancholi, T Klingberg, W Zhang, R Prizak… - Molecular systems …, 2021 - embopress.org
It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two
major control points are recruitment of RNA polymerase II (Pol II) into a paused state, and …