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 …
Homeodomain proteins: an update
TR Bürglin, M Affolter - Chromosoma, 2016 - Springer
Here, we provide an update of our review on homeobox genes that we wrote together with
Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have …
Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have …
Geometric deep learning of protein–DNA binding specificity
Predicting protein–DNA binding specificity is a challenging yet essential task for
understanding gene regulation. Protein–DNA complexes usually exhibit binding to a …
understanding gene regulation. Protein–DNA complexes usually exhibit binding to a …
Low affinity binding site clusters confer hox specificity and regulatory robustness
In animals, Hox transcription factors define regional identity in distinct anatomical domains.
How Hox genes encode this specificity is a paradox, because different Hox proteins bind …
How Hox genes encode this specificity is a paradox, because different Hox proteins bind …
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 …
Genetic determinants and epigenetic effects of pioneer-factor occupancy
Transcription factors (TFs) direct developmental transitions by binding to target DNA
sequences, influencing gene expression and establishing complex gene-regultory networks …
sequences, influencing gene expression and establishing complex gene-regultory networks …
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 …
Deconvolving the recognition of DNA shape from sequence
Protein-DNA binding is mediated by the recognition of the chemical signatures of the DNA
bases and the 3D shape of the DNA molecule. Because DNA shape is a consequence of …
bases and the 3D shape of the DNA molecule. Because DNA shape is a consequence of …
Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models
Transcription factors (TF s) achieve DNA‐binding specificity through contacts with functional
groups of bases (base readout) and readout of structural properties of the double helix …
groups of bases (base readout) and readout of structural properties of the double helix …
Evolving insights on how cytosine methylation affects protein–DNA binding
Many anecdotal observations exist of a regulatory effect of DNA methylation on gene
expression. However, in general, the underlying mechanisms of this effect are poorly …
expression. However, in general, the underlying mechanisms of this effect are poorly …