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 …

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 …

Enhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion

S Zhang, N Übelmesser, M Barbieri, A Papantonis - Nature genetics, 2023 - nature.com
Homotypic chromatin interactions and loop extrusion are thought to be the two main drivers
of mammalian chromosome folding. Here we tested the role of RNA polymerase II (RNAPII) …

Recent evidence that TADs and chromatin loops are dynamic structures

AS Hansen, C Cattoglio, X Darzacq, R Tjian - Nucleus, 2018 - Taylor & Francis
Mammalian genomes are folded into spatial domains, which regulate gene expression by
modulating enhancer-promoter contacts. Here, we review recent studies on the structure …

[HTML][HTML] Chromosome conformation capture and beyond: toward an integrative view of chromosome structure and function

RP McCord, N Kaplan, L Giorgetti - Molecular cell, 2020 - cell.com
Rapidly developing technologies have recently fueled an exciting era of discovery in the
field of chromosome structure and nuclear organization. In addition to chromosome …

TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer

M Tu, L Klein, E Espinet, T Georgomanolis, F Wegwitz… - Nature cancer, 2021 - nature.com
Large-scale genomic profiling of pancreatic cancer (PDAC) has revealed two distinct
subtypes:'classical'and 'basal-like'. Their variable coexistence within the stromal immune …

RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis

S Zhang, N Übelmesser, N Josipovic, G Forte… - Science …, 2021 - science.org
Mammalian chromosomes are three-dimensional entities shaped by converging and
opposing forces. Mitotic cell division induces marked chromosome condensation, but …

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

RA Beagrie, CJ Thieme, C Annunziatella, C Baugher… - Nature …, 2023 - nature.com
Technology for measuring 3D genome topology is increasingly important for studying gene
regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and …

Enhancer–promoter specificity in gene transcription: molecular mechanisms and disease associations

MJ Friedman, T Wagner, H Lee… - … & Molecular Medicine, 2024 - nature.com
Although often located at a distance from their target gene promoters, enhancers are the
primary genomic determinants of temporal and spatial transcriptional specificity in …

3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering

J Han, Z Zhang, K Wang - Molecular Cytogenetics, 2018 - Springer
It is well known that the chromosomes are organized in the nucleus and this spatial
arrangement of genome play a crucial role in gene regulation and genome stability. Different …