chipseq identified sequences

Question

[mkh]

HI All,

I am not familiar with chip-seq data analysis. I would like to know why the chip-seq identified DNA sequences for one specific protein binding site has different lengths? for example the chipseq binding regions for protein A could be between 100-2000 bps? How the binding sites ranges determined from chip-seq data?

Thanks, Morteza

Answer 1

[Arup Ghosh]

ChIP-seq data is mostly used for finding DNA binding motifs. The transcription factor binding motifs are generally short 8-12bp DNA sequences. Once motif has been identified the sequence is used as a quay for databases like JASPER, TRANSFAC® to find known transcription factor binding events.