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 …

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

CR Clapier, J Iwasa, BR Cairns… - Nature reviews Molecular …, 2017 - nature.com
Cells utilize diverse ATP-dependent nucleosome-remodelling complexes to carry out
histone sliding, ejection or the incorporation of histone variants, suggesting that different …

Understanding nucleosome dynamics and their links to gene expression and DNA replication

WKM Lai, BF Pugh - Nature reviews Molecular cell biology, 2017 - nature.com
Advances in genomics technology have provided the means to probe myriad chromatin
interactions at unprecedented spatial and temporal resolution. This has led to a profound …

Energy-driven genome regulation by ATP-dependent chromatin remodellers

S Eustermann, AB Patel, KP Hopfner, Y He… - … Reviews Molecular Cell …, 2024 - nature.com
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA
replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re) arrange …

The interaction landscape between transcription factors and the nucleosome

F Zhu, L Farnung, E Kaasinen, B Sahu, Y Yin, B Wei… - Nature, 2018 - nature.com
Nucleosomes cover most of the genome and are thought to be displaced by transcription
factors in regions that direct gene expression. However, the modes of interaction between …

[HTML][HTML] 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 …

[HTML][HTML] Genomic nucleosome organization reconstituted with pure proteins

N Krietenstein, M Wal, S Watanabe, B Park… - Cell, 2016 - cell.com
Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but
their individual contributions are obfuscated by the complex in vivo milieu of factor …

[HTML][HTML] Steroid receptors reprogram FoxA1 occupancy through dynamic chromatin transitions

EE Swinstead, TB Miranda, V Paakinaho, S Baek… - Cell, 2016 - cell.com
The estrogen receptor (ER), glucocorticoid receptor (GR), and forkhead box protein 1
(FoxA1) are significant factors in breast cancer progression. FoxA1 has been implicated in …

Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens

N Liscovitch-Brauer, A Montalbano, J Deng… - Nature …, 2021 - nature.com
CRISPR screens have been used to connect genetic perturbations with changes in gene
expression and phenotypes. Here we describe a CRISPR-based, single-cell combinatorial …

[HTML][HTML] RSC-associated subnucleosomes define MNase-sensitive promoters in yeast

S Brahma, S Henikoff - Molecular cell, 2019 - cell.com
The classic view of nucleosome organization at active promoters is that two well-positioned
nucleosomes flank a nucleosome-depleted region (NDR). However, this view has been …