Transcription factors and 3D genome conformation in cell-fate decisions

R Stadhouders, GJ Filion, T Graf - Nature, 2019 - nature.com
How cells adopt different identities has long fascinated biologists. Signal transduction in
response to environmental cues results in the activation of transcription factors that …

Formation of chromatin subcompartments by phase separation

F Erdel, K Rippe - Biophysical journal, 2018 - cell.com
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 …

[HTML][HTML] Organization of chromatin by intrinsic and regulated phase separation

BA Gibson, LK Doolittle, MWG Schneider, LE Jensen… - Cell, 2019 - cell.com
Eukaryotic chromatin is highly condensed but dynamically accessible to regulation and
organized into subdomains. We demonstrate that reconstituted chromatin undergoes …

Condensed chromatin behaves like a solid on the mesoscale in vitro and in living cells

H Strickfaden, TO Tolsma, A Sharma, DA Underhill… - Cell, 2020 - cell.com
The association of nuclear DNA with histones to form chromatin is essential for temporal and
spatial control of eukaryotic genomes. In this study, we examined the physical state of …

Dynamic organization of chromatin domains revealed by super-resolution live-cell imaging

T Nozaki, R Imai, M Tanbo, R Nagashima, S Tamura… - Molecular cell, 2017 - cell.com
The eukaryotic genome is organized within cells as chromatin. For proper information
output, higher-order chromatin structures can be regulated dynamically. How such structures …

Liquid–liquid phase separation in chromatin

K Rippe - Cold Spring Harbor perspectives in biology, 2022 - cshperspectives.cshlp.org
In eukaryotic cells, protein and RNA factors involved in genome activities like transcription,
RNA processing, DNA replication, and repair accumulate in self-organizing membraneless …

Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions

SE Farr, EJ Woods, JA Joseph, A Garaizar… - Nature …, 2021 - nature.com
Liquid–liquid phase separation (LLPS) is an important mechanism that helps explain the
membraneless compartmentalization of the nucleus. Because chromatin compaction and …

Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation

K Joron, JO Viegas, L Haas-Neill, S Bier, P Drori… - Nature …, 2023 - nature.com
Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced
fluorescence microscopy, FPs can report on additional intracellular variables. One variable …

Uncovering the forces between nucleosomes using DNA origami

JJ Funke, P Ketterer, C Lieleg, S Schunter, P Korber… - Science …, 2016 - science.org
Revealing the energy landscape for nucleosome association may contribute to the
understanding of higher-order chromatin structures and their impact on genome regulation …

Dynamic chromatin organization without the 30-nm fiber

K Maeshima, S Ide, M Babokhov - Current opinion in cell biology, 2019 - Elsevier
Chromatin in eukaryotic cells is a negatively charged polymer composed of DNA, histones,
and various associated proteins. Over the past ten years, our view of chromatin has shifted …