Generating specificity in genome regulation through transcription factor sensitivity to chromatin

L Isbel, RS Grand, D Schübeler - Nature Reviews Genetics, 2022 - nature.com
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …

Determinants of nucleosome positioning

K Struhl, E Segal - Nature structural & molecular biology, 2013 - nature.com
Nucleosome positioning is critical for gene expression and most DNA-related processes.
Here we review the dominant patterns of nucleosome positioning that have been observed …

[HTML][HTML] H2A. Z-containing nucleosomes mediate the thermosensory response in Arabidopsis

SV Kumar, PA Wigge - Cell, 2010 - cell.com
Plants are highly sensitive to temperature and can perceive a difference of as little as 1° C.
How temperature is sensed and integrated in development is unknown. In a forward genetic …

Regulation of Amino Acid, Nucleotide, and Phosphate Metabolism in Saccharomyces cerevisiae

PO Ljungdahl, B Daignan-Fornier - Genetics, 2012 - academic.oup.com
Ever since the beginning of biochemical analysis, yeast has been a pioneering model for
studying the regulation of eukaryotic metabolism. During the last three decades, the …

Morphogen gradients: from generation to interpretation

KW Rogers, AF Schier - Annual review of cell and …, 2011 - annualreviews.org
Morphogens are long-range signaling molecules that pattern develo** tissues in a
concentration-dependent manner. The graded activity of morphogens within tissues …

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

E Sharon, Y Kalma, A Sharp, T Raveh-Sadka… - Nature …, 2012 - nature.com
Despite extensive research, our understanding of the rules according to which cis-regulatory
sequences are converted into gene expression is limited. We devised a method for …

Defining mechanisms that regulate RNA polymerase II transcription in vivo

NJ Fuda, MB Ardehali, JT Lis - Nature, 2009 - nature.com
In the eukaryotic genome, the thousands of genes that encode messenger RNA are
transcribed by a molecular machine called RNA polymerase II. Analysing the distribution …

Determinants and dynamics of genome accessibility

O Bell, VK Tiwari, NH Thomä, D Schübeler - Nature Reviews Genetics, 2011 - nature.com
In eukaryotes, all DNA-templated reactions occur in the context of chromatin. Nucleosome
packaging inherently restricts DNA accessibility for regulatory proteins but also provides an …

Chromatin repressive complexes in stem cells, development, and cancer

A Laugesen, K Helin - Cell stem cell, 2014 - cell.com
The chromatin environment is essential for the correct specification and preservation of cell
identity through modulation and maintenance of transcription patterns. Many chromatin …

The logic of chromatin architecture and remodelling at promoters

BR Cairns - Nature, 2009 - nature.com
The regulation of gene transcription involves a dynamic balance between packaging
regulatory sequences into chromatin and allowing transcriptional regulators access to these …