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 …

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 …

Developmental enhancers and chromosome topology

EEM Furlong, M Levine - Science, 2018 - science.org
Developmental enhancers mediate on/off patterns of gene expression in specific cell types
at particular stages during metazoan embryogenesis. They typically integrate multiple …

LHX2-and LDB1-mediated trans interactions regulate olfactory receptor choice

K Monahan, A Horta, S Lomvardas - Nature, 2019 - nature.com
The genome is partitioned into topologically associated domains and genomic
compartments with shared chromatin valence. This architecture is constrained by the DNA …

YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle

JC Lam, NG Aboreden, SC Midla, S Wang, A Huang… - Nature Genetics, 2024 - nature.com
Few transcription factors have been examined for their direct roles in physically connecting
enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells …

[HTML][HTML] Cohesin-dependent and-independent mechanisms mediate chromosomal contacts between promoters and enhancers

MJ Thiecke, G Wutz, M Muhar, W Tang, S Bevan… - Cell reports, 2020 - cell.com
It is currently assumed that 3D chromosomal organization plays a central role in
transcriptional control. However, depletion of cohesin and CTCF affects the steady-state …

BE-PLUS: a new base editing tool with broadened editing window and enhanced fidelity

W Jiang, S Feng, S Huang, W Yu, G Li, G Yang, Y Liu… - Cell Research, 2018 - nature.com
Base editor (BE), containing a cytidine deaminase and catalytically defective Cas9, has
been widely used to perform base editing. However, the narrow editing window of BE limits …

Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS

Y Hu, DS Figueroa, Z Zhang, M Veselits… - Cell, 2023 - cell.com
A generic level of chromatin organization generated by the interplay between cohesin and
CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage …

Predicting enhancer‐promoter interaction from genomic sequence with deep neural networks

S Singh, Y Yang, B Póczos, J Ma - Quantitative Biology, 2019 - Wiley Online Library
Background In the human genome, distal enhancers are involved in regulating target genes
through proximal promoters by forming enhancer‐promoter interactions. Although recently …