Eukaryotic transcriptional dynamics: from single molecules to cell populations

A Coulon, CC Chow, RH Singer, DR Larson - Nature reviews genetics, 2013 - nature.com
Transcriptional regulation is achieved through combinatorial interactions between regulatory
elements in the human genome and a vast range of factors that modulate the recruitment …

Visualizing transcription factor dynamics in living cells

Z Liu, R Tjian - Journal of Cell Biology, 2018 - rupress.org
The assembly of sequence-specific enhancer-binding transcription factors (TFs) at cis-
regulatory elements in the genome has long been regarded as the fundamental mechanism …

An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors

DA Garcia, TA Johnson, DM Presman, G Fettweis… - Molecular cell, 2021 - cell.com
Transcription factors (TFs) regulate gene expression by binding to specific consensus motifs
within the local chromatin context. The mechanisms by which TFs navigate the nuclear …

A benchmark for chromatin binding measurements in live cells

D Mazza, A Abernathy, N Golob, T Morisaki… - Nucleic acids …, 2012 - academic.oup.com
Live-cell measurement of protein binding to chromatin allows probing cellular biochemistry
in physiological conditions, which are difficult to mimic in vitro. However, different studies …

An orange fluorescent protein with a large Stokes shift for single-excitation multicolor FCCS and FRET imaging

DM Shcherbakova, MA Hink, L Joosen… - Journal of the …, 2012 - ACS Publications
Multicolor imaging based on genetically encoded fluorescent proteins (FPs) is a powerful
approach to study several dynamic processes in a live cell. We report a monomeric orange …

DNase footprint signatures are dictated by factor dynamics and DNA sequence

MH Sung, MJ Guertin, S Baek, GL Hager - Molecular cell, 2014 - cell.com
Genomic footprinting has emerged as an unbiased discovery method for transcription factor
(TF) occupancy at cognate DNA in vivo. A basic premise of footprinting is that sequence …

Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth

N Bellotto, J Agudo-Canalejo, R Colin, R Golestanian… - Elife, 2022 - elifesciences.org
Inside prokaryotic cells, passive translational diffusion typically limits the rates with which
cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular …

A guide to changing paradigms of glucocorticoid receptor function—a model system for genome regulation and physiology

S Vettorazzi, D Nalbantoglu, JCM Gebhardt… - The FEBS …, 2022 - Wiley Online Library
The glucocorticoid receptor (GR) is a bona fide ligand‐regulated transcription factor. Cloned
in the 80s, the GR has become one of the best‐studied and clinically most relevant members …

Quantitative theory for the diffusive dynamics of liquid condensates

L Hubatsch, LM Jawerth, C Love, J Bauermann… - Elife, 2021 - elifesciences.org
Key processes of biological condensates are diffusion and material exchange with their
environment. Experimentally, diffusive dynamics are typically probed via fluorescent labels …

Fluorescence recovery after photobleaching in colloidal science: introduction and application

AA Moud - ACS Biomaterials Science & Engineering, 2022 - ACS Publications
FRAP (fluorescence recovery after photo bleaching) is a method for determining diffusion in
material science. In industrial applications such as medications, foods, Medtech, hygiene …