Precise dissection of DNA–protein interactions is essential for elucidating the recognition
basis, dynamics and gene regulation mechanism. However, global profiling of weak and …

Chromatin immunoprecipitation (ChIP-chip and ChIP-seq) assays identify where proteins
bind throughout a genome. However, DNA contamination and DNA fragmentation …

Studies of genome regulation routinely use high-throughput DNA sequencing approaches to
determine where specific proteins interact with DNA, and they rely on DNA amplification and …

Transcription factors (TFs) regulate gene expression in both prokaryotes and eukaryotes by
recognizing and binding to specific DNA promoter sequences. In higher eukaryotes, it …

Recent advances in experimental and computational methodologies are enabling ultra-high
resolution genome-wide profiles of protein–DNA binding events. For example, the ChIP-exo …

Conspectus Dynamic protein–DNA interactions constitute highly robust cellular machineries
to fulfill cellular functions. A vast number of studies have focused on how DNA-binding …

Genome-wide mapping of transcription factor binding is generally performed by chemical
protein–DNA crosslinking, followed by chromatin immunoprecipitation and deep sequencing …

Deciphering gene regulatory network architecture amounts to the identification of the
regulators, conditions in which they act, genes they regulate, cis-acting motifs they bind …

To improve chemical cross-linking of proteins coupled with mass spectrometry (CXMS), we
developed a lysine-targeted enrichable cross-linker containing a biotin tag for affinity …

Evaluating the specificity spectra of DNA binding molecules is a nontrivial challenge that
hinders the ability to decipher gene regulatory networks or engineer molecules that act on …