Genome control by SMC complexes

C Hoencamp, BD Rowland - Nature Reviews Molecular Cell Biology, 2023 - nature.com
Many cellular processes require large-scale rearrangements of chromatin structure.
Structural maintenance of chromosomes (SMC) protein complexes are molecular machines …

TADs: Dynamic structures to create stable regulatory functions

JA da Costa-Nunes, D Noordermeer - Current Opinion in Structural Biology, 2023 - Elsevier
Mammalian chromosomes are organized at different length scales within the cell nucleus.
Topologically Associating Domains (TADs) are structural units of 3D genome organization …

Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition

SE Murphy, AN Boettiger - Nature genetics, 2024 - nature.com
Polycomb group proteins have a critical role in silencing transcription during development. It
is commonly proposed that Polycomb-dependent changes in genome folding, which …

Polymer folding through active processes recreates features of genome organization

A Goychuk, D Kannan… - Proceedings of the …, 2023 - National Acad Sciences
From proteins to chromosomes, polymers fold into specific conformations that control their
biological function. Polymer folding has long been studied with equilibrium thermodynamics …

NIPBL and cohesin: new take on a classic tale

D Alonso-Gil, A Losada - Trends in Cell Biology, 2023 - cell.com
Cohesin folds the genome in dynamic chromatin loops and holds the sister chromatids
together. NIPBL Scc2 is currently considered the cohesin loader, a role that may need …

Temporally correlated active forces drive segregation and enhanced dynamics in chromosome polymers

S Brahmachari, T Markovich, FC MacKintosh… - PRX Life, 2024 - APS
Understanding the mechanisms governing the structure and dynamics of flexible polymers
like chromosomes, especially the signatures of motor-driven active processes, is of great …

A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks

E Al-Jibury, JWD King, Y Guo, B Lenhard… - Nature …, 2023 - nature.com
The organisation of the genome in nuclear space is an important frontier of biology.
Chromosome conformation capture methods such as Hi-C and Micro-C produce genome …

Loop extrusion rules: the next generation

F Corsi, E Rusch, A Goloborodko - Current Opinion in Genetics & …, 2023 - Elsevier
Highlights•Cohesin loop extrusion is the key mechanism of 3D genome organization in
interphase of vertebrates.•Models of loop extrusion infer locations and dynamics of cohesin …

Theory of chromatin organization maintained by active loop extrusion

B Chan, M Rubinstein - Proceedings of the National …, 2023 - National Acad Sciences
The active loop extrusion hypothesis proposes that chromatin threads through the cohesin
protein complex into progressively larger loops until reaching specific boundary elements …

Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging

T Sabaté, B Lelandais, E Bertrand… - Nucleic Acids …, 2023 - academic.oup.com
Genome-wide chromosome conformation capture (Hi-C) has revealed the organization of
chromatin into topologically associating domains (TADs) and loops, which are thought to …