Transcriptional architecture of the mammalian circadian clock

JS Takahashi - Nature Reviews Genetics, 2017‏ - nature.com
Circadian clocks are endogenous oscillators that control 24-hour physiological and
behavioural processes in organisms. These cell-autonomous clocks are composed of a …

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 …

Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization

EP Nora, A Goloborodko, AL Valton, JH Gibcus… - Cell, 2017‏ - cell.com
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly
understood. The transcription factor CTCF is a candidate regulator of chromosomal …

3D structures of individual mammalian genomes studied by single-cell Hi-C

TJ Stevens, D Lando, S Basu, LP Atkinson, Y Cao… - Nature, 2017‏ - nature.com
The folding of genomic DNA from the beads-on-a-string-like structure of nucleosomes into
higher-order assemblies is crucially linked to nuclear processes. Here we calculate 3D …

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 …

Polyploidy, the nucleotype, and novelty: the impact of genome doubling on the biology of the cell

JJ Doyle, JE Coate - International journal of plant sciences, 2019‏ - journals.uchicago.edu
Polyploidy is a key mechanism of genome evolution and speciation, particularly in plants.
Many aspects of polyploidy have been elucidated with the tools that have become available …

[HTML][HTML] Navigating challenges and opportunities in multi-omics integration for personalized healthcare

AE Mohr, CP Ortega-Santos, CM Whisner… - Biomedicines, 2024‏ - mdpi.com
The field of multi-omics has witnessed unprecedented growth, converging multiple scientific
disciplines and technological advances. This surge is evidenced by a more than doubling in …

Transcription organizes euchromatin via microphase separation

L Hilbert, Y Sato, K Kuznetsova, T Bianucci… - Nature …, 2021‏ - nature.com
In eukaryotes, DNA is packed inside the cell nucleus in the form of chromatin, which consists
of DNA, proteins such as histones, and RNA. Euchromatin, which is permissive for …

Super-resolution microscopy with single molecules in biology and beyond–essentials, current trends, and future challenges

L Möckl, WE Moerner - Journal of the American Chemical …, 2020‏ - ACS Publications
Single-molecule super-resolution microscopy has developed from a specialized technique
into one of the most versatile and powerful imaging methods of the nanoscale over the past …

[HTML][HTML] The physics of active polymers and filaments

RG Winkler, G Gompper - The journal of chemical physics, 2020‏ - pubs.aip.org
Active matter agents consume internal energy or extract energy from the environment for
locomotion and force generation. Already, rather generic models, such as ensembles of …