Estimating transcription factor bindability on DNA

DNA replication efficiency depends on transcription factor-binding sites.

Naturally arising variants of simian virus 40 (SV40), generated by serial passage of the virus at high multiplicities of infection, provide important insight into the role of transcription factor-binding sites in enhancing DNA replication. Although the variants that arise from numerous recombination events are the result of selective pressure to replicate more efficiently than the other variant...

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...

Are DNA transcription factor proteins maxwellian demons?

Transcription factor (TF) proteins rapidly locate unique target sites on long genomic DNA molecules--and bind to them--during gene regulation. The search mechanism is known to involve a combination of three-dimensional diffusion through the bulk of the cell and one-dimensional sliding diffusion along the DNA. It is believed that the surprisingly high target binding rates of TF proteins relies o...

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...