[HTML][HTML] Deciphering the multi-scale, quantitative cis-regulatory code

S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …

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 …

Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

VY Goel, MK Huseyin, AS Hansen - Nature genetics, 2023 - nature.com
Although enhancers are central regulators of mammalian gene expression, the mechanisms
underlying enhancer–promoter (EP) interactions remain unclear. Chromosome …

[HTML][HTML] Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

THS Hsieh, C Cattoglio, E Slobodyanyuk, AS Hansen… - Nature …, 2022 - nature.com
It remains unclear why acute depletion of CTCF (CCCTC-binding factor) and cohesin only
marginally affects expression of most genes despite substantially perturbing three …

[HTML][HTML] 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 …

Enhancer selectivity in space and time: from enhancer–promoter interactions to promoter activation

JH Yang, AS Hansen - Nature Reviews Molecular Cell Biology, 2024 - nature.com
The primary regulators of metazoan gene expression are enhancers, originally functionally
defined as DNA sequences that can activate transcription at promoters in an orientation …

Cohesin is required for long-range enhancer action at the Shh locus

L Kane, I Williamson, IM Flyamer, Y Kumar… - Nature structural & …, 2022 - nature.com
The regulatory landscapes of developmental genes in mammals can be complex, with
enhancers spread over many hundreds of kilobases. It has been suggested that three …

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 …

[HTML][HTML] Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries

LH Chang, S Ghosh, A Papale, JM Luppino… - Nature …, 2023 - nature.com
Abstract Topologically Associating Domains (TADs) separate vertebrate genomes into
insulated regulatory neighborhoods that focus genome-associated processes. TADs are …