Pioneer transcription factors initiating gene network changes

KS Zaret - Annual review of genetics, 2020 - annualreviews.org
Pioneer transcription factors have the intrinsic biochemical ability to scan partial DNA
sequence motifs that are exposed on the surface of a nucleosome and thus access silent …

Deep learning for cellular image analysis

E Moen, D Bannon, T Kudo, W Graf, M Covert… - Nature …, 2019 - nature.com
Recent advances in computer vision and machine learning underpin a collection of
algorithms with an impressive ability to decipher the content of images. These deep learning …

Transcription factors and 3D genome conformation in cell-fate decisions

R Stadhouders, GJ Filion, T Graf - Nature, 2019 - nature.com
How cells adopt different identities has long fascinated biologists. Signal transduction in
response to environmental cues results in the activation of transcription factors that …

The axon initial segment: an updated viewpoint

C Leterrier - Journal of Neuroscience, 2018 - Soc Neuroscience
At the base of axons sits a unique compartment called the axon initial segment (AIS). The
AIS generates and shapes the action potential before it is propagated along the axon …

Nanometer-resolution tracking of single cargo reveals dynein motor mechanisms

CS Peng, Y Zhang, Q Liu, GE Marti… - Nature Chemical …, 2024 - nature.com
Cytoplasmic dynein is essential for intracellular transport. Despite extensive in vitro
characterizations, how the dynein motors transport vesicles by processive steps in live cells …

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 …

Cohesin prevents cross-domain gene coactivation

P Dong, S Zhang, V Gandin, L Xie, L Wang… - Nature Genetics, 2024 - nature.com
The contrast between the disruption of genome topology after cohesin loss and the lack of
downstream gene expression changes instigates intense debates regarding the structure …

Kinetic principles underlying pioneer function of GAGA transcription factor in live cells

X Tang, T Li, S Liu, J Wisniewski, Q Zheng… - Nature structural & …, 2022 - nature.com
How pioneer factors interface with chromatin to promote accessibility for transcription control
is poorly understood in vivo. Here, we directly visualize chromatin association by the …

Two-parameter mobility assessments discriminate diverse regulatory factor behaviors in chromatin

J Lerner, PA Gomez-Garcia, RL McCarthy, Z Liu… - Molecular cell, 2020 - cell.com
Enzymatic probes of chromatin structure reveal accessible versus inaccessible chromatin
states, while super-resolution microscopy reveals a continuum of chromatin compaction …

Single-molecule tracking (SMT): a window into live-cell transcription biochemistry

L Dahal, N Walther, R Tjian, X Darzacq… - Biochemical Society …, 2023 - portlandpress.com
How molecules interact governs how they move. Single-molecule tracking (SMT) thus
provides a unique window into the dynamic interactions of biomolecules within live cells …