Deciphering the multi-scale, quantitative cis-regulatory code
S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
The Mediator complex as a master regulator of transcription by RNA polymerase II
WF Richter, S Nayak, J Iwasa, DJ Taatjes - Nature Reviews Molecular …, 2022 - nature.com
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits,
controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining …
controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining …
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
C Bravo González-Blas, S De Winter, G Hulselmans… - Nature …, 2023 - nature.com
Joint profiling of chromatin accessibility and gene expression in individual cells provides an
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …
The spatial organization of transcriptional control
A Hafner, A Boettiger - Nature Reviews Genetics, 2023 - nature.com
In animals, the sequences for controlling gene expression do not concentrate just at the
transcription start site of genes, but are frequently thousands to millions of base pairs distal …
transcription start site of genes, but are frequently thousands to millions of base pairs distal …
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 …
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 …
The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication
How distal cis-regulatory elements (eg, enhancers) communicate with promoters remains an
unresolved question of fundamental importance. Although transcription factors and cofactors …
unresolved question of fundamental importance. Although transcription factors and cofactors …
Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability
E McArthur, JA Capra - The American Journal of Human Genetics, 2021 - cell.com
Topologically associating domains (TADs) are fundamental units of three-dimensional (3D)
nuclear organization. The regions bordering TADs—TAD boundaries—contribute to the …
nuclear organization. The regions bordering TADs—TAD boundaries—contribute to the …
New insights into genome folding by loop extrusion from inducible degron technologies
Chromatin folds into dynamic loops that often span hundreds of kilobases and physically
wire distant loci together for gene regulation. These loops are continuously created …
wire distant loci together for gene regulation. These loops are continuously created …