Transcription Factor Binding to Replicated DNA

Linking Transcription Factor Expression with DNA Binding

Evolution of transcription factor DNA binding sites.

In bioinformatics, binding of transcription regulatory factors to the cognate binding sites is usually described by sequence-specific binding energy, which is estimated from a training sample of sites. This model implies that all binding sites with binding energy above some threshold are functional and site sequence variations should be considered neutral until they do not reduce this energy be...

Transcription factor-DNA binding: beyond binding site motifs.

Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-regulatory elements in promoter and enhancer DNA. While studies of TF-DNA binding have focused on TFs' intrinsic preferences for primary nucleotide sequence motifs, recent studies have elucidated additional layers of complexity that modulate TF-DNA binding. In this review, we discuss technological developme...

DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity.

Transcription factors (TFs) are regulatory proteins that bind DNA in promoter regions of the genome and either promote or repress gene expression. Here, we predict analytically that enhanced homooligonucleotide sequence correlations, such as poly(dA:dT) and poly(dC:dG) tracts, statistically enhance nonspecific TF-DNA binding affinity. This prediction is generic and qualitatively independent of ...

DNA binding by the ribosomal DNA transcription factor rrn3 is essential for ribosomal DNA transcription.

The human homologue of yeast Rrn3 is an RNA polymerase I-associated transcription factor that is essential for ribosomal DNA (rDNA) transcription. The generally accepted model is that Rrn3 functions as a bridge between RNA polymerase I and the transcription factors bound to the committed template. In this model Rrn3 would mediate an interaction between the mammalian Rrn3-polymerase I complex an...