The spatial organization of transcriptional control

A Hafner, A Boettiger - Nature Reviews Genetics, 2023 - nature.com
In animals, the sequences for controlling gene expression do not concentrate just at the
transcription start site of genes, but are frequently thousands to millions of base pairs distal …

Looping the genome with SMC complexes

E Kim, R Barth, C Dekker - Annual review of biochemistry, 2023 - annualreviews.org
SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily
conserved family of motor proteins that hold sister chromatids together and fold genomes …

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

HL Harris, H Gu, M Olshansky, A Wang… - Nature …, 2023 - nature.com
Nuclear compartments are prominent features of 3D chromatin organization, but sequencing
depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally …

Enhancer–promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness

S Chakraborty, N Kopitchinski, Z Zuo, A Eraso… - Nature …, 2023 - nature.com
How enhancers activate their distal target promoters remains incompletely understood. Here
we dissect how CTCF-mediated loops facilitate and restrict such regulatory interactions …

[PDF][PDF] 3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

CM Uyehara, E Apostolou - Cell reports, 2023 - cell.com
The spatiotemporal control of gene expression is dependent on the activity of cis-acting
regulatory sequences, called enhancers, which regulate target genes over variable genomic …

New insights into genome folding by loop extrusion from inducible degron technologies

E de Wit, EP Nora - Nature Reviews Genetics, 2023 - nature.com
Chromatin folds into dynamic loops that often span hundreds of kilobases and physically
wire distant loci together for gene regulation. These loops are continuously created …

Size limits the sensitivity of kinetic schemes

JA Owen, JM Horowitz - Nature Communications, 2023 - nature.com
Living things benefit from exquisite molecular sensitivity in many of their key processes,
including DNA replication, transcription and translation, chemical sensing, and …

The Mediator complex regulates enhancer-promoter interactions

S Ramasamy, A Aljahani, MA Karpinska… - Nature Structural & …, 2023 - nature.com
Enhancer-mediated gene activation generally requires physical proximity between
enhancers and their target gene promoters. However, the molecular mechanisms by which …

[HTML][HTML] The role of loop extrusion in enhancer-mediated gene activation

MA Karpinska, AM Oudelaar - Current Opinion in Genetics & Development, 2023 - Elsevier
Gene expression patterns in complex multicellular organisms are regulated by enhancers,
which communicate with their target gene promoters in three-dimensional (3D) chromatin …

Computational methods for analysing multiscale 3D genome organization

Y Zhang, L Boninsegna, M Yang, T Misteli… - Nature Reviews …, 2024 - nature.com
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 …