Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences

DT McSwiggen, M Mir, X Darzacq… - Genes & …, 2019 - genesdev.cshlp.org
The idea that liquid–liquid phase separation (LLPS) may be a general mechanism by which
molecules in the complex cellular milieu may self-organize has generated much excitement …

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 …

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

WK Cho, JH Spille, M Hecht, C Lee, C Li, V Grube… - Science, 2018 - science.org
Models of gene control have emerged from genetic and biochemical studies, with limited
consideration of the spatial organization and dynamics of key components in living cells. We …

A general method to optimize and functionalize red-shifted rhodamine dyes

JB Grimm, AN Tkachuk, L Xie, H Choi, B Mohar… - Nature …, 2020 - nature.com
Expanding the palette of fluorescent dyes is vital to push the frontier of biological imaging.
Although rhodamine dyes remain the premier type of small-molecule fluorophore owing to …

Mechanisms regulating zygotic genome activation

KN Schulz, MM Harrison - Nature Reviews Genetics, 2019 - nature.com
Following fertilization, the two specified gametes must unite to create an entirely new
organism. The genome is initially transcriptionally quiescent, allowing the zygote to be …

The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication

JP Karr, JJ Ferrie, R Tjian, X Darzacq - Genes & Development, 2022 - genesdev.cshlp.org
How distal cis-regulatory elements (eg, enhancers) communicate with promoters remains an
unresolved question of fundamental importance. Although transcription factors and cofactors …

Complex multi-enhancer contacts captured by genome architecture mapping

RA Beagrie, A Scialdone, M Schueler, DCA Kraemer… - Nature, 2017 - nature.com
The organization of the genome in the nucleus and the interactions of genes with their
regulatory elements are key features of transcriptional control and their disruption can cause …

A general method to fine-tune fluorophores for live-cell and in vivo imaging

JB Grimm, AK Muthusamy, Y Liang, TA Brown… - Nature …, 2017 - nature.com
Pushing the frontier of fluorescence microscopy requires the design of enhanced
fluorophores with finely tuned properties. We recently discovered that incorporation of four …

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

W Li, D Notani, MG Rosenfeld - Nature Reviews Genetics, 2016 - nature.com
Networks of regulatory enhancers dictate distinct cell identities and cellular responses to
diverse signals by instructing precise spatiotemporal patterns of gene expression. However …

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

KM Harlen, LS Churchman - Nature reviews Molecular cell biology, 2017 - nature.com
The carboxy-terminal domain (CTD) extends from the largest subunit of RNA polymerase II
(Pol II) as a long, repetitive and largely unstructured polypeptide chain. Throughout the …