Nonlinear control of transcription through enhancer–promoter interactions
Chromosome structure in mammals is thought to regulate transcription by modulating three-
dimensional interactions between enhancers and promoters, notably through CTCF …
dimensional interactions between enhancers and promoters, notably through CTCF …
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 …
we dissect how CTCF-mediated loops facilitate and restrict such regulatory interactions …
Genome organization controls transcriptional dynamics during development
Past studies offer contradictory claims for the role of genome organization in the regulation
of gene activity. Here, we show through high-resolution chromosome conformation analysis …
of gene activity. Here, we show through high-resolution chromosome conformation analysis …
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1
It remains unclear why acute depletion of CTCF (CCCTC-binding factor) and cohesin only
marginally affects expression of most genes despite substantially perturbing three …
marginally affects expression of most genes despite substantially perturbing three …
Function and evolution of the loop extrusion machinery in animals
E Kabirova, A Nurislamov, A Shadskiy… - International Journal of …, 2023 - mdpi.com
Structural maintenance of chromosomes (SMC) complexes are essential proteins found in
genomes of all cellular organisms. Essential functions of these proteins, such as mitotic …
genomes of all cellular organisms. Essential functions of these proteins, such as mitotic …
Establishing and maintaining Hox profiles during spinal cord development
The chromosomally-arrayed Hox gene family plays central roles in embryonic patterning
and the specification of cell identities throughout the animal kingdom. In vertebrates, the …
and the specification of cell identities throughout the animal kingdom. In vertebrates, the …
Boundary stacking interactions enable cross-TAD enhancer–promoter communication during limb development
TC Hung, DM Kingsley, AN Boettiger - Nature Genetics, 2024 - nature.com
Although promoters and their enhancers are frequently contained within a topologically
associating domain (TAD), some developmentally important genes have their promoter and …
associating domain (TAD), some developmentally important genes have their promoter and …
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions
Comprehensive enhancer discovery is challenging because most enhancers, especially
those contributing to complex diseases, have weak effects on gene expression. Our gene …
those contributing to complex diseases, have weak effects on gene expression. Our gene …
Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1
THS Hsieh, C Cattoglio, E Slobodyanyuk, AS Hansen… - Biorxiv, 2021 - biorxiv.org
It remains unclear why acute depletion of CTCF and cohesin only marginally affects
expression of most genes despite substantially perturbing 3D genome folding at the level of …
expression of most genes despite substantially perturbing 3D genome folding at the level of …
Enhancer–promoter interactions can form independently of genomic distance and be functional across TAD boundaries
D Balasubramanian, P Borges Pinto… - Nucleic Acids …, 2024 - academic.oup.com
Abstract Topologically Associating Domains (TADs) have been suggested to facilitate and
constrain enhancer–promoter interactions. However, the role of TAD boundaries in …
constrain enhancer–promoter interactions. However, the role of TAD boundaries in …