Long-range enhancer–promoter contacts in gene expression control

S Schoenfelder, P Fraser - Nature Reviews Genetics, 2019 - nature.com
Spatiotemporal gene expression programmes are orchestrated by transcriptional
enhancers, which are key regulatory DNA elements that engage in physical contacts with …

Organizational principles of 3D genome architecture

MJ Rowley, VG Corces - Nature Reviews Genetics, 2018 - nature.com
Studies of 3D chromatin organization have suggested that chromosomes are hierarchically
organized into large compartments composed of smaller domains called topologically …

[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 …

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 …

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

N Kubo, H Ishii, X Xiong, S Bianco… - Nature structural & …, 2021 - nature.com
The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive the
formation of chromatin loops and topologically associating domains, but its role in gene …

The relationship between genome structure and function

AM Oudelaar, DR Higgs - Nature Reviews Genetics, 2021 - nature.com
Precise patterns of gene expression in metazoans are controlled by three classes of
regulatory elements: promoters, enhancers and boundary elements. During differentiation …

Predicting 3D genome folding from DNA sequence with Akita

G Fudenberg, DR Kelley, KS Pollard - Nature methods, 2020 - nature.com
In interphase, the human genome sequence folds in three dimensions into a rich variety of
locus-specific contact patterns. Cohesin and CTCF (CCCTC-binding factor) are key …

[HTML][HTML] YY1 is a structural regulator of enhancer-promoter loops

AS Weintraub, CH Li, AV Zamudio, AA Sigova… - Cell, 2017 - cell.com
There is considerable evidence that chromosome structure plays important roles in gene
control, but we have limited understanding of the proteins that contribute to structural …

[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 …

[HTML][HTML] Resolving the 3D landscape of transcription-linked mammalian chromatin folding

THS Hsieh, C Cattoglio, E Slobodyanyuk, AS Hansen… - Molecular cell, 2020 - cell.com
Whereas folding of genomes at the large scale of epigenomic compartments and
topologically associating domains (TADs) is now relatively well understood, how chromatin …