Transcriptional enhancers: from properties to genome-wide predictions

D Shlyueva, G Stampfel, A Stark - Nature Reviews Genetics, 2014 - nature.com
Cellular development, morphology and function are governed by precise patterns of gene
expression. These are established by the coordinated action of genomic regulatory …

Formaldehyde crosslinking: a tool for the study of chromatin complexes

EA Hoffman, BL Frey, LM Smith, DT Auble - Journal of Biological Chemistry, 2015 - jbc.org
Formaldehyde has been used for decades to probe macromolecular structure and function
and to trap complexes, cells, and tissues for further analysis. Formaldehyde crosslinking is …

The quantitative and condition-dependent Escherichia coli proteome

A Schmidt, K Kochanowski, S Vedelaar, E Ahrné… - Nature …, 2016 - nature.com
Measuring precise concentrations of proteins can provide insights into biological processes.
Here we use efficient protein extraction and sample fractionation, as well as state-of-the-art …

[HTML][HTML] Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources

GW Li, D Burkhardt, C Gross, JS Weissman - Cell, 2014 - cell.com
Quantitative views of cellular functions require precise measures of rates of biomolecule
production, especially proteins—the direct effectors of biological processes. Here, we …

[HTML][HTML] Probing the stochastic, motor-driven properties of the cytoplasm using force spectrum microscopy

M Guo, AJ Ehrlicher, MH Jensen, M Renz, JR Moore… - Cell, 2014 - cell.com
Molecular motors in cells typically produce highly directed motion; however, the aggregate,
incoherent effect of all active processes also creates randomly fluctuating forces, which drive …

Chromatin organization drives the search mechanism of nuclear factors

M Mazzocca, A Loffreda, E Colombo, T Fillot… - Nature …, 2023 - nature.com
Nuclear factors rapidly scan the genome for their targets, but the role of nuclear organization
in such search is uncharted. Here we analyzed how multiple factors explore chromatin …

Single-molecule dynamics of enhanceosome assembly in embryonic stem cells

J Chen, Z Zhang, L Li, BC Chen, A Revyakin, B Hajj… - Cell, 2014 - cell.com
Enhancer-binding pluripotency regulators (Sox2 and Oct4) play a seminal role in embryonic
stem (ES) cell-specific gene regulation. Here, we combine in vivo and in vitro single …

Enhancers: five essential questions

LA Pennacchio, W Bickmore, A Dean… - Nature Reviews …, 2013 - nature.com
Although enhancers are crucial and widespread gene-regulatory elements, we are far from
a complete understanding of how they function or their importance in areas such as disease …

Transcription factor dynamics: one molecule at a time

K Wagh, DA Stavreva, A Upadhyaya… - Annual Review of Cell …, 2023 - annualreviews.org
Cells must tightly regulate their gene expression programs and yet rapidly respond to acute
biochemical and biophysical cues within their environment. This information is transmitted to …

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

JCM Gebhardt, DM Suter, R Roy, ZW Zhao… - Nature …, 2013 - nature.com
Imaging single fluorescent proteins in living mammalian cells is challenged by out-of-focus
fluorescence excitation. To reduce out-of-focus fluorescence we developed reflected light …