Genome folding through loop extrusion by SMC complexes

IF Davidson, JM Peters - Nature reviews Molecular cell biology, 2021 - nature.com
Genomic DNA is folded into loops and topologically associating domains (TADs), which
serve important structural and regulatory roles. It has been proposed that these genomic …

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 …

CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion

IF Davidson, R Barth, M Zaczek, J van der Torre… - Nature, 2023 - nature.com
In eukaryotes, genomic DNA is extruded into loops by cohesin. By restraining this process,
the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating …

[HTML][HTML] The energetics and physiological impact of cohesin extrusion

L Vian, A Pękowska, SSP Rao, KR Kieffer-Kwon… - Cell, 2018 - cell.com
Cohesin extrusion is thought to play a central role in establishing the architecture of
mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its …

A pliable mediator acts as a functional rather than an architectural bridge between promoters and enhancers

L El Khattabi, H Zhao, J Kalchschmidt, N Young… - Cell, 2019 - cell.com
While Mediator plays a key role in eukaryotic transcription, little is known about its
mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays …

CTCF shapes chromatin structure and gene expression in health and disease

B Dehingia, M Milewska, M Janowski, A Pękowska - EMBO reports, 2022 - embopress.org
CCCTC‐binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional
regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations …

Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues

SJ Heo, S Thakur, X Chen, C Loebel, B Xia… - Nature biomedical …, 2023 - nature.com
Abstract Changes in the micro-environment of fibrous connective tissue can lead to
alterations in the phenotypes of tissue-resident cells, yet the underlying mechanisms are …

Dual roles of poly (dA: dT) tracts in replication initiation and fork collapse

A Tubbs, S Sridharan, N van Wietmarschen, Y Maman… - Cell, 2018 - cell.com
Replication origins, fragile sites, and rDNA have been implicated as sources of
chromosomal instability. However, the defining genomic features of replication origins and …

Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma

R Zeid, MA Lawlor, E Poon, JM Reyes, M Fulciniti… - Nature …, 2018 - nature.com
Amplification of the locus encoding the oncogenic transcription factor MYCN is a defining
feature of high-risk neuroblastoma. Here we present the first dynamic chromatin and …

[HTML][HTML] Chromatin jets define the properties of cohesin-driven in vivo loop extrusion

Y Guo, E Al-Jibury, R Garcia-Millan, K Ntagiantas… - Molecular Cell, 2022 - cell.com
Complex genomes show intricate organization in three-dimensional (3D) nuclear space.
Current models posit that cohesin extrudes loops to form self-interacting domains delimited …