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 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 …
Dynamics of CTCF-and cohesin-mediated chromatin loo** revealed by live-cell imaging
Animal genomes are folded into loops and topologically associating domains (TADs) by
CTCF and loop-extruding cohesins, but the live dynamics of loop formation and stability …
CTCF and loop-extruding cohesins, but the live dynamics of loop formation and stability …
Cohesin and CTCF control the dynamics of chromosome folding
In mammals, interactions between sequences within topologically associating domains
enable control of gene expression across large genomic distances. Yet it is unknown how …
enable control of gene expression across large genomic distances. Yet it is unknown how …
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 selectivity in space and time: from enhancer–promoter interactions to promoter activation
The primary regulators of metazoan gene expression are enhancers, originally functionally
defined as DNA sequences that can activate transcription at promoters in an orientation …
defined as DNA sequences that can activate transcription at promoters in an orientation …
CTCF shapes chromatin structure and gene expression in health and disease
CCCTC‐binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional
regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations …
regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations …
Mechanisms of chromosome folding and nuclear organization: their interplay and open questions
Microscopy and genomic approaches provide detailed descriptions of the three-dimensional
folding of chromosomes and nuclear organization. The fundamental question is how activity …
folding of chromosomes and nuclear organization. The fundamental question is how activity …
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin
It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two
major control points are recruitment of RNA polymerase II (Pol II) into a paused state, and …
major control points are recruitment of RNA polymerase II (Pol II) into a paused state, and …
Real-time single-molecule imaging of transcriptional regulatory networks in living cells
Gene regulatory networks drive the specific transcriptional programmes responsible for the
diversification of cell types during the development of multicellular organisms. Although our …
diversification of cell types during the development of multicellular organisms. Although our …