KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity.

ABSTRACT: It is difficult to exhaustively screen all possible DNA binding sequences for a given transcription factor (TF). Here, we developed the KaScape method, in which TFs bind to all possible DNA sequences in the same DNA pool where DNA sequences are prepared by randomized oligo synthesis and the random length can be adjusted to a length such as 4, 5, 6, or 7. After separating bound from unbound double-stranded DNAs (dsDNAs), their sequences are determined by next-generation sequencing. To demonstrate the relative binding affinities of all possible DNA sequences determined by KaScape, we developed three-dimensional KaScape viewing software based on a K-mer graph. We applied KaScape to 12 plant TF family AtWRKY proteins and found that all AtWRKY proteins bound to the core sequence GAC with simila

SUBMITTER: Chen H 

PROVIDER: S-EPMC10547764 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature