The present invention provides, inter alia, methods and kits for identifying where a polypeptide of interest binds in a genome. The methods include a) carrying out a chromatin immunoprecipitation coupled to exonuclease digestion (ChIP-exo) process with an antibody against the polypeptide of interest; (b) extracting a polynucleotide fragment to which the polypeptide of interest binds; (c) carrying out a library preparation protocol adapted from an individual nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) process on the ChIP-exo processed polynucleotide fragment; and (d) sequencing the resulting polynucleotides. The kits include: (a) reagents sufficient to carry out ChIP-exo; (b) reagents sufficient to carry out the library preparation protocol adapted from the iCLIP process; and (c) instructions for use.