Transcription factors (TFs) achieve DNA-binding specificity through contacts with functional groups of bases (base readout) and readout of structural properties of the double helix (shape readout). Currently, it remains unclear whether DNA shape readout is utilized by only a few selected TF families, or whether this mechanism is used extensively by most TF families. We resequenced data from previously published HT-SELEX experiments, the most extensive mammalian TF–DNA binding data available to date. Using these data, we demonstrated the contributions of DNA shape readout across diverse TF families and its importance in core motif-flanking regions. Statistical machine-learning models combined with feature-selection techniques helped to revea...
Genomic analyses often involve scanning for potential transcription factor (TF) binding sites using ...
The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expres...
SummaryAlthough the proteins that read the gene regulatory code, transcription factors (TFs), have b...
SummaryInteractions of transcription factors (TFs) with DNA comprise a complex interplay between bas...
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. ...
SummaryInteractions of transcription factors (TFs) with DNA comprise a complex interplay between bas...
Motivation: Recognition of specific DNA sequences is a central mechanism by which transcription fact...
2014-11-03Gene regulation is orchestrated by the binding of transcription factors (TFs) to their spe...
Protein–DNA recognition is a critical component of gene regulatory processes but the underlying mole...
The binding of transcription factors (TFs) is essential for gene expression. One important character...
2018-08-06Protein–DNA binding is a fundamental component of gene regulatory processes, but it is sti...
Transcription factor (TF) proteins recognize a small number of DNA sequences with high specificity a...
Predicting how and where proteins, especially transcription factors (TFs), interact with DNA is an i...
Transcriptional regulation is imperative for proper development of multicellular organisms, and disr...
Numerous efforts are underway to determine gene regulatory networks that describe physical relations...
Genomic analyses often involve scanning for potential transcription factor (TF) binding sites using ...
The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expres...
SummaryAlthough the proteins that read the gene regulatory code, transcription factors (TFs), have b...
SummaryInteractions of transcription factors (TFs) with DNA comprise a complex interplay between bas...
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. ...
SummaryInteractions of transcription factors (TFs) with DNA comprise a complex interplay between bas...
Motivation: Recognition of specific DNA sequences is a central mechanism by which transcription fact...
2014-11-03Gene regulation is orchestrated by the binding of transcription factors (TFs) to their spe...
Protein–DNA recognition is a critical component of gene regulatory processes but the underlying mole...
The binding of transcription factors (TFs) is essential for gene expression. One important character...
2018-08-06Protein–DNA binding is a fundamental component of gene regulatory processes, but it is sti...
Transcription factor (TF) proteins recognize a small number of DNA sequences with high specificity a...
Predicting how and where proteins, especially transcription factors (TFs), interact with DNA is an i...
Transcriptional regulation is imperative for proper development of multicellular organisms, and disr...
Numerous efforts are underway to determine gene regulatory networks that describe physical relations...
Genomic analyses often involve scanning for potential transcription factor (TF) binding sites using ...
The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expres...
SummaryAlthough the proteins that read the gene regulatory code, transcription factors (TFs), have b...