A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting

NC Lammers, YJ Kim, J Zhao, HG Garcia - Current opinion in cell biology, 2020 - Elsevier
Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours;
however, state-of-the-art measurements have revealed that many of the molecular …

Gene regulation in and out of equilibrium

F Wong, J Gunawardena - Annual review of biophysics, 2020 - annualreviews.org
Determining whether and how a gene is transcribed are two of the central processes of life.
The conceptual basis for understanding such gene regulation arose from pioneering …

Size limits the sensitivity of kinetic schemes

JA Owen, JM Horowitz - Nature Communications, 2023 - nature.com
Living things benefit from exquisite molecular sensitivity in many of their key processes,
including DNA replication, transcription and translation, chemical sensing, and …

Multimodal transcriptional control of pattern formation in embryonic development

NC Lammers, V Galstyan, A Reimer… - Proceedings of the …, 2020 - National Acad Sciences
Predicting how interactions between transcription factors and regulatory DNA sequence
dictate rates of transcription and, ultimately, drive developmental outcomes remains an open …

Topologically constrained fluctuations and thermodynamics regulate nonequilibrium response

G Fernandes Martins, JM Horowitz - Physical Review E, 2023 - APS
The limits on a system's response to external perturbations inform our understanding of how
physical properties can be shaped by microscopic characteristics. Here, we derive …

Allosteric conformational ensembles have unlimited capacity for integrating information

JW Biddle, R Martinez-Corral, F Wong, J Gunawardena - Elife, 2021 - elifesciences.org
Integration of binding information by macromolecular entities is fundamental to cellular
functionality. Recent work has shown that such integration cannot be explained by pairwise …

Precision of tissue patterning is controlled by dynamical properties of gene regulatory networks

K Exelby, E Herrera-Delgado, LG Perez… - …, 2021 - journals.biologists.com
During development, gene regulatory networks allocate cell fates by partitioning tissues into
spatially organised domains of gene expression. How the sharp boundaries that delineate …

Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient

S Alamos, A Reimer, C Westrum, MA Turner, P Talledo… - Cell systems, 2023 - cell.com
How enhancers interpret morphogen gradients to generate gene expression patterns is a
central question in developmental biology. Recent studies have proposed that enhancers …

A matter of time: Formation and interpretation of the Bicoid morphogen gradient

A Huang, TE Saunders - Current topics in developmental biology, 2020 - Elsevier
Spatially distributed signaling molecules, known as morphogens, provide spatial information
during development. A host of different morphogens have now been identified, from …

A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute

J Desponds, M Vergassola, AM Walczak - Elife, 2020 - elifesciences.org
Cell fate decisions in the fly embryo are rapid: hunchback genes decide in minutes whether
nuclei follow the anterior/posterior developmental blueprint by reading out positional …