DNA-binding properties of FOXP3 transcription factor

Domain Requirements and Sequence Specificity of DNA Binding for the Forkhead Transcription Factor FOXP3

The forkhead, winged-helix transcription factor FOXP3 is preferentially expressed in T regulatory (Treg) cells and is critical for their immunosuppressive function. Mutations that abolish FOXP3 function lead to systemic autoimmunity in mice and humans. However, the manner by which FOXP3 recognizes cognate DNA elements is unclear. Here we identify an in vitro optimized DNA sequence to assess FOX...

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...

Bioinformatics Approach for Transcription Factor Binding Properties

A random forest classifier for transcription factor binding properties. (Fig. 1). O ne of the central questions in molecular genetics regards the mechanisms of transcriptional regulation , particularly how transcription factors (TFs) regulate expression of target genes with specific TF binding sites (TFBSs). Identifying TFBSs would permit a more comprehensive and quantitative mapping of the reg...

Linking Transcription Factor Expression with DNA Binding

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...