Mechanisms of enhancer action: the known and the unknown

A Panigrahi, BW O'Malley - Genome biology, 2021 - Springer
Differential gene expression mechanisms ensure cellular differentiation and plasticity to
shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential …

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 …

Transcription shapes 3D chromatin organization by interacting with loop extrusion

EJ Banigan, W Tang… - Proceedings of the …, 2023 - National Acad Sciences
Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into
numerous loops.“Loop extrusion” can be impeded by chromatin-bound factors, such as …

Loo** the genome with SMC complexes

E Kim, R Barth, C Dekker - Annual review of biochemistry, 2023 - annualreviews.org
SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily
conserved family of motor proteins that hold sister chromatids together and fold genomes …

Complex multi-enhancer contacts captured by genome architecture map**

RA Beagrie, A Scialdone, M Schueler, DCA Kraemer… - Nature, 2017 - nature.com
The organization of the genome in the nucleus and the interactions of genes with their
regulatory elements are key features of transcriptional control and their disruption can cause …

The 3D genome as moderator of chromosomal communication

J Dekker, L Mirny - Cell, 2016 - cell.com
Proper expression of genes requires communication with their regulatory elements that can
be located elsewhere along the chromosome. The physics of chromatin fibers imposes a …

Enhancer regulation of transcriptional bursting parameters revealed by forced chromatin loo**

CR Bartman, SC Hsu, CCS Hsiung, A Raj, GA Blobel - Molecular cell, 2016 - cell.com
Mammalian genes transcribe RNA not continuously, but in bursts. Transcriptional output can
be modulated by altering burst fraction or burst size, but how regulatory elements control …

Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

THS Hsieh, G Fudenberg, A Goloborodko, OJ Rando - Nature methods, 2016 - nature.com
Abstract We present Micro-C XL, an improved method for analysis of chromosome folding at
mononucleosome resolution. Using long crosslinkers and isolation of insoluble chromatin …

Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III

Y Jiang, J Huang, K Lun, B Li, H Zheng, Y Li, R Zhou… - Genome biology, 2020 - Springer
Background The relationship between transcription and the 3D chromatin structure is
debated. Multiple studies have shown that transcription affects global Cohesin binding and …

High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription

A Bressin, O Jasnovidova, M Arnold… - Nature …, 2023 - nature.com
Gene transcription by RNA polymerase II (Pol II) is under control of promoters and distal
regulatory elements known as enhancers. Enhancers are themselves transcribed by Pol II …