Energy-driven genome regulation by ATP-dependent chromatin remodellers
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA
replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re) arrange …
replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re) arrange …
[HTML][HTML] Absence of a simple code: how transcription factors read the genome
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
[PDF][PDF] 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 …
their individual contributions are obfuscated by the complex in vivo milieu of factor …
MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding
Polycomb-mediated repression of gene expression is essential for development, with a
pivotal role played by trimethylation of histone H3 lysine 27 (H3K27me3), which is deposited …
pivotal role played by trimethylation of histone H3 lysine 27 (H3K27me3), which is deposited …
Quantum annealing versus classical machine learning applied to a simplified computational biology problem
Transcription factors regulate gene expression, but how these proteins recognize and
specifically bind to their DNA targets is still debated. Machine learning models are effective …
specifically bind to their DNA targets is still debated. Machine learning models are effective …
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints
Q He, J Johnston, J Zeitlinger - Nature biotechnology, 2015 - nature.com
Understanding how eukaryotic enhancers are bound and regulated by specific
combinations of transcription factors is still a major challenge. To better map transcription …
combinations of transcription factors is still a major challenge. To better map transcription …
A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
The adaptation of the CRISPR-Cas9 system as a genome editing technique has generated
much excitement in recent years owing to its ability to manipulate targeted genes and …
much excitement in recent years owing to its ability to manipulate targeted genes and …
Quantitative modeling of transcription factor binding specificities using DNA shape
DNA binding specificities of transcription factors (TFs) are a key component of gene
regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs …
regulatory processes. Underlying mechanisms that explain the highly specific binding of TFs …
Protein–DNA binding: complexities and multi-protein codes
Binding of proteins to particular DNA sites across the genome is a primary determinant of
specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded …
specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded …
[PDF][PDF] Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
Transcription factors (TFs) preferentially bind sites contained in regions of computationally
predicted high nucleosomal occupancy, suggesting that nucleosomes are gatekeepers of TF …
predicted high nucleosomal occupancy, suggesting that nucleosomes are gatekeepers of TF …