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 …

Determining chromatin architecture with Micro Capture-C

JC Hamley, H Li, N Denny, D Downes, JOJ Davies - Nature Protocols, 2023 - nature.com
Abstract Micro Capture-C (MCC) is a chromatin conformation capture (3C) method for
visualizing reproducible three-dimensional contacts of specified regions of the genome at …

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 …

Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq

Z Liu, Y Chen, Q Xia, M Liu, H Xu, Y Chi, Y Deng… - Science, 2023 - science.org
Much progress has been made recently in single-cell chromosome conformation capture
technologies. However, a method that allows simultaneous profiling of chromatin …

Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning

E Ing-Simmons, R Vaid, XY Bing, M Levine… - Nature …, 2021 - nature.com
The relationship between chromatin organization and gene regulation remains unclear.
While disruption of chromatin domains and domain boundaries can lead to misexpression of …

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

A Aljahani, P Hua, MA Karpinska, K Quililan… - Nature …, 2022 - nature.com
Enhancers and promoters predominantly interact within large-scale topologically
associating domains (TADs), which are formed by loop extrusion mediated by cohesin and …

[HTML][HTML] Super-enhancers include classical enhancers and facilitators to fully activate gene expression

JW Blayney, H Francis, A Rampasekova, B Camellato… - Cell, 2023 - cell.com
Super-enhancers are compound regulatory elements that control expression of key cell
identity genes. They recruit high levels of tissue-specific transcription factors and co …

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 …

BET inhibition disrupts transcription but retains enhancer-promoter contact

NT Crump, E Ballabio, L Godfrey, R Thorne… - Nature …, 2021 - nature.com
Enhancers are DNA sequences that enable complex temporal and tissue-specific regulation
of genes in higher eukaryotes. Although it is not entirely clear how enhancer-promoter …

Transcription factor competition at the γ-globin promoters controls hemoglobin switching

N Liu, S Xu, Q Yao, Q Zhu, Y Kai, JY Hsu, P Sakon… - Nature …, 2021 - nature.com
BCL11A, the major regulator of fetal hemoglobin (HbF, α2γ2) level, represses γ-globin
expression through direct promoter binding in adult erythroid cells in a switch to adult …